I think I may have made a breakthrough in finding the problem with the timeouts.
[Update]
Nope. Or at least not as big a one as I thought...
Still timing out.
[Update]
Seeing what happens now...
[Update, infuriated]
OK, now I've blown it. I screwed up my comments and individual entry templates, and I didn't back it up. I've had it.
Testing to see whether comments still time out.
Well, it timed out but after backing up I didn't have to hit "refresh" to see the comment ...
Well, it's (very) minor progress. It does tell me that there is indeed some subtle problem with the template, though. I replaced part of it with boilerplate MT, and we did get a minor change in behavior...
I don't know how you did it. I still had to back up and refresh.
How are you moving your data files onto the webserver? Are you using FTP? If your using FTP and have the xfer mode set to auto you might want to strictly specify data xfer only. It is possible your data files are getting corrupted during the transfer across the network.
I don't move files on to the server (at least to fix this problem). MT has a web utility to modify templates. But when I do upload files, I use scp. When I have to edit files, I do it in the shell with vi.
So in brief, no, file corruption is not the issue. Would that it were that simple...
Testing another comment...
RSS is working now.
Well, RSS was working. It's broken again.
"Would that it were that simple..."
Hey, many a times have I seen the benefits of keeping it simple stupid when it comes to resolving an issue. Often the fix is lurking just beyond the proboscis.