Well, the multi-select bug appears to be intermittent. It has happened to me a few times since I first reported it. Here is the sequence I usually take:
1) I get a new batch from BT
2) I copy these files into my anime directory
3) I start AniDB
4) I wait for it to be disconnected
5) I go to Explorer Right click the folders and say Hash with AniDB
6) After all the new file appear, I click start
7) After it is done hashing, renaming, creqing I go to the Known Files Tab

I expand the series of interest
9) I multi-select (ctrl-click or shift-click) the episodes (usually 5) and add to my-list.
10) I select something else and wait; sometimes they will all change color, sometimes only one will
BTW, it does not appear to be a refresh problem, because if I exit and check the CGI or AOM later it still does not show up in mylist.
I keep looking for patterns, but I have not found anything yet. I thought maybe it happened with the first selection I did, but I did it again on the remaining 4 episodes and it happened again. Then I thought it might happen right after the hashing and renaming, so I exited, reloaded AOM and tried it on the remaining 3, and it happened again. I then did the remaing 2 and it did both of them.
One time I think it may have been a communication problem with AniDB because in the log it appeared to be stuck, it did not get to the disconnected line. The last time around, though, the log looked fine, the communications appeared to comlete.
I will continue to test (as long as I keep getting BT batches) and see if I can find a pattern.
I have noticed on startup I get a variable number of lines that say:
! Illegal file input data or access denied, ignoring...
I have assumed this is because of unimplemented portions, but I thought I would mention it to make sure it is not an indicator of something else going on.