@Matthew: all of your screen shots have sky behind them. This issue is when cloud form below ground (eg. when using super flat with more than 128 layers). It will not happen with non-super flat world generation because the clouds are always above ground.
Can confirm mine carts not flickering in 12w49a.
Didn't really look at other blocks in details, but impression is that they fall more smoothly.
I've created MC-3784 for the third part of this: seeing the sun through the clouds while underground.
@Peter: There is a separate bug report for the mine cart sound problems... which were in 1.4.2 and earlier (IIRC).
EDIT: This one: MC-1642.
Short video that (sort of) shows the problem. On screen it appears far more extreme.
@Kumasasa: no.
This is much more sever, and happens to all sides of the cart, looking to the sides as well as both forward and backwards.
@Allaiyah Weyn: What has that got to do with random flames? (Hint: change your profile to not auto-watch, then unwatch any issues you are watching).
Just tried 1.4.5: and I could not re-create. Seems it is at least reduced in severity.
Confirmed in 1.4.5 pre-release.
... and just tried the same with an oak sampling and did not re-create.
So there is a species dependency.
Just tried again Added before and after shots. Note the single wall block on the right front corner with a leaf block below that was wall.
NB. This is using a larch sampling in single player creative.
1.4.4 pre-release.
Not fixed in 1.4.4: wall around the tree was all the same height before bone meal applied to sapling.
As can be seen in screen shot 2012-11-12_16.37.10.png most of the top row of wall has been replaced by the tree.
Continues in 1.4.4.
I'm getting this in 1.4.4.
Also if cart sound (on long run) is glitching it plays normally when paused!
Confirmed. Rather distracting when sprinting along a mine tunnel with torches placed along it.
@Aden: There were fixes to walls in 1.4.3 (eg. MC-1332) so likely this issue was introduced while fixing some other aspect of wall behaviour.
@Kumasasa Am I correct in understanding that – if the flickering was removed by having the item frame in front of the chest lid – you would not consider the placement of item frame in front of the chest lid a bug?
IOW you are proposing that an opening chest lid passing behind any item frames places on a block one block above and behind the chest.
I consider any flickering as an irrelevant consequence of the underlying bug: the chest lid is not in front of the item frame.
@Maarten: It seems your comment worked 🙂