Looks like tv.com has ordered the listings for those shows based on their production code, rather than air date (which it used to be). TVRename is using the air-date to sort them and number them into episode numbers.
The weird thing is if you look at
ReBoot, season 4, on tv.com, the first two episodes are:
"Daemon Rising (1)" First aired: 10/19/2001 Production Code: v4.1.1
"Cross Nodes (2)" First aired: 10/10/2001 Production Code: v4.1.2
So, according to tv.com, the second part of the two parter was aired before the first part.
A similar thing is happening for X-men. Your Xena & Gossip Girl eps are getting renamed because tv.com has changed the episode titles. The other ones look (without going to tv.com) like they're suffering from the same date problem as ReBoot.
For tracing what's going on, the episode guide in TVRename is built from what it thinks is going on (not just copied directly out of tv.com's pages), so the order, episode numbers, and dates there are based on what it thinks is "right". If you go to the bug report, turn on just "Folder Scan" and hit "Create", you'll see a list of your media library and, in brackets, what season+episode TVRename is associating with each file in it.
To fix out-of-order episodes from TVRename, go to the "Shows & Folders" tab, edit the show that has the problem (e.g. ReBoot), click "Add" beside rules, choose "Swap" and put in "1" and "2". Go to the episode guide, hit "refresh" at the top, and it should be fixed (until tv.com unjumbles them, then you'll just have to remove the rule again).
