Gabe Hansen

I actually put my server on a hiatus due to this issue, we were all at the point where we had just started going to the nether rather regularly, and then the next snapshot started killing us.

A MINIMAL WORKAROUND I'VE FOUND:
Disclaimer: while not very efficient, it at least fixes suffocation, though I haven't had any issues with porting back and forth either (My server's personal experience!). the procedure must also be repeated for all portals, that you want functional. You can temporarily disable portals you don't want used in the meantime. This worked for my server, I suppose I should say success may vary, though. Worth a try.

1: Copy the map over to single player.
2: Go to the coordinates of the portal in both dimensions and write them down.
3: In creative, clear a large (like 10x10x10 area, just to be safe) at the coordinates in the OPPOSITE dimension of each coordinate. (if overworld portal is 30, 5, 62; then clear those coordinates in the nether, and vice versa.)
4: Copy edited map back over to server.

What bug this gets past is when using a portal, the game initially puts you at the coordinates of the dimension you just left, and this commonly means that when teleporting to the nether, the game attempts to teleport you into inside a wall, which sends other red flags up that attempt to cancel out the port as if you never ported to begin with (this happens before the server can realize that where you should have been ported to was actually clear, but its undone before it can actually fix that), though since you were ported to inside a wall, you also take a tiny bit of suffocation damage each time. When it teleports you back, you are considered at the coordinates of the portal you just left (the actual portals coords, not where the game originally mentally put you) So then you are once again stuck in a wall, even if everything is properly rendered as if you were at the appropriate coordinates. Clearing the areas makes it so that you are no longer accidentally placed in a wall, and no longer sends the red flags of error to cancel out the portal, which now gives the game enough time to actually know you are where you are supposed to be when taking a nether portal.

I switched my home server to allow nether to see if it was still effecting us, and it sadly is, so I have once again temporarily disabled the nether. My buddy gets caught in the loop and dies without fail if he tries to go to the nether.

I made a backup and switched maps to a new map (with a clean new SMP folder with all new files from the snapshot, not reusing any files from older worlds or snapshots), it still was an issue so my personal experience says it is not a save corruption issue.

I had to disable the Nether on my family server for the time being. happens to everyone on my server using snapshot 43c (yes, I have a map backup without snapshots just in case). Seems to be Multiplayer only, I haven't had an issue in Single Player at all, but its both Creative mode or survival mode it doesn't matter. Endless teleporting loop, being snapped back into the portal after leaving it and immediately being ported to the other dimension. My brother and my friend both died of suffocation damage due to taking a small amount of damage every time and endless looping til death. Upon respawning back in, no items can be found in either dimension.