Updated to include that armor stands are also destroyed by lightning strikes.
When you say the bug is with a specific nether portal, do you mean that if you create another one nearby so that it links to the same one in the nether, that you don't get the issue with things going through that one? Do you get the same issue with a portal to the nether that is far enough away that an entirely new naturally-linked set is created? Were guardians or other mobs at any point previously going through the portal without issues? If you let non-guardian mobs go through the portal, does that cause any issue as well? I'd look into those questions as a starting point to get the details needed for others to replicate your issue. You might try running a fresh world and then going through and setting things up so that you are able to list the steps you took to replicate the issue yourself, and posting those once you are able to.
I wasn't able to replicate the issue, at least in singleplayer. I spawned a ton of guardians next to a nether portal, and a bunch of them went into the nether without issue. I followed them through, and they were flopping around in the nether. I also had no issues with throwing items into the nether.
The mods probably did check themselves to see if the drivers resolved the issue for them as well, though they may not have explicitly stated that. I know I had it, and updating to the beta drivers resolved the issue for me. The drivers being in beta is beside the point in any case, as the fact that one of the fixes listed by AMD in their updated drivers was to solve this issue indicates that the issue was primarily on their end. This takes it from a bug report for Minecraft to a bug report for AMD's graphics drivers. Hence why this ticket and similar issues are marked as "invalid".
The issue is still present in 1.8.1 pre-4. Attached is an example from one pillar, and these are all over the place throughout the area.
It's probably due to lightning strikes. It looks like it is raining in your picture, and lightning probably struck the roof near the corner of the room there and took out the frames. See https://bugs.mojang.com/browse/MC-38307 for more details on that.
A little further testing shows it was fixed between 14w29b and 14w30c.
I just tested this again in 14w31a, and it looks like the issue has now been fixed.
I've included a couple of screenshots that visually illustrate what the area effect of lightning covers. Red represents the block that the lightning strikes, the orange shows what is within the effect of the lightning(inclusive of the area occupied by the orange blocks themselves), the green shows area outside the effects, and the blue represents a cutaway view of the blocks making up a home.
Something I've also noticed is that in addition to destroying item frames and paintings within the orange area, lightning can also injure or kill mobs that are within a structure as well.
I've noticed this same bug is still present in 1.7.5 and 14w11b. To give some more detail on the nature of the bug:
For example, I can create a four-tier pyramid, then set the beacon to provide the primary power of the strength boost and the secondary power of regeneration, and then break the fourth, third, and second levels of the pyramid, and the primary power of strength will continue to refresh, although only out to 20 blocks, and the secondary power will not refresh.
If I then repair the pyramid's second layer, the range of the primary power will extend out to 30 blocks. Repairing the third layer will increase the range to 40 blocks. And repairing the fourth layer will return the beacon to full functionality. If I break the first level(leaving the beacon block itself intact), then the primary power will stop, but if I then restore only the first level of the pyramid, the beacon will continue to provide the primary power of strength out to 20 blocks.
Ultimately, the beacon is properly checking to see if it should apply the secondary power, and how far a range it should apply primary or secondary powers out to, but is not checking to see if the TYPE of primary power it is set to provide is still supported by the appropriate number of layers required to initially select it.
I just tested this again in snapshot 14w11b, and it is still in effect.
This was explicitly added as feature.
That looks like normal portal behavior. If you remain standing in the portal after coming through, it doesn't just send you back and forth endlessly. You need to step completely out of the portal, then back into it in order for it to transport you back to the nether/overworld.
My best estimation is that the lightning strike area of effect is about 3 blocks to the sides and 3 blocks down. Possibly 3 blocks up as well, but I haven't tested for that. As I mentioned, in the cases I've seen, it also deleted or knocked down the frames the items were in as well, though considering my small sample size, I wouldn't rule out that in some cases it may just delete items from within some frames.
But taking a closer look at your screenshot, it seems that there is at least a one-square gap between the top level maps and what is possibly the roof, which wouldn't explain the bottom frame, which seems like it would be outside the area-effect range that I've observed.
Included are a couple of screenshots of the setup I had been using, where I had been on the far side of the bars from the cows. Had you eaten just prior to running the test? I duplicated your setup and numbers of cows, and it seemed to take about 10 minutes before the saturation from eating a single steak was depleted. Once the saturation was gone, with the ~20 cows, it took ~55 seconds to deplete 1 point of hunger. When I increased the number of cows in your setup to ~80, it took ~30 seconds to deplete 1 point of hunger.
It may have been the result of lightning striking nearby, which I've witnessed to have deleted items in frames, though in the cases I've seen, this also deleted or knocked down the item frames.
I've now attached a copy of the forced crash report.
Further testing shows that this also affects paintings as well.
It was in vanilla 1.6.2 in SMP when I was encountering this.
Good to hear. Seems like the best solution, as I'm not even sure how you'd go about determining blocks providing protection anyway, considering all the possibilities like a pillar between the strike point, or something under an overhang that gets hit, but that has no walls, etc.