I don't know if this has already been covered, but I'm having this problem:

My Main/Alt section is configured properly to the best of my knowledge, and it branches characters into groups as it should.

However, whenever data is uploaded then it all gets reset and I have to go back and click "Update Relations" again each time there is an update.
Is this normal?

no, it isn't. It should be updating relations during an upload.

What is your site link?
Are any per-guild configurations set?

http://godsoffortitude.freehostia.com/theguild

Per-guild configs.. Do you mean having a guild specified in the Update Rules section?

No, I mean in the per-guild config section of the memberslist configuration.

Can you get me an update log from a CP update?

I might've fixed it, I'll find out in a few mins.
I did find a valid problem though..

Sometimes people have funky characters in their names. We have a person whose main is named Sunstär. All of her alt's notes are just like the rest of the guild's, they say Sunstär's Alt.
The Main/Alt parser works on every other character in the guild except for her alts, which it considers MA.
Does Roster 2 not take into consideration the growing trend of nontraditional characters?

You can see an example of this at http://godsoffortitude.com/theguild

Roster2 takes into consideration the trend of us still supporting php 4.3 and 5.0, which don't support \pL in regexes.
If you have php 4.4+ or 5.1+, feel free to use \pL instead of \w. That'll fix the problem.

\pL certainly fixed the character problem and everything is working as it should. Not using the per-guild setting also remedied the main/alt relations not updating automatically as I wanted them to.
Thanks so much!

Relations are still borked while using per-guild settings, however. I uploaded last night using UniUploader, and all 3 guilds I host had incorrect relations afterwards.

I can send you a log file when I get home from work if necessary.

I couldn't tell from the SVN logs; has this been looked at? Guild relations are being lost every time anyone updates with either UU or manually.

All of them go away when someone ups without guild data?

Oh, and can you tell me how many characters are in your roster, and how many records are in the roster_addons_memberslist_alts table?

From what I'm seeing, all of them go away if I upload *with* guild data.

I just doublechecked with a brand new characterprofiler.lua file and it's definitely NOT updating relations on upload. There are 231 characters in the guild and 364 rows in addons_memberslist_alts (there are 2 other guilds sharing that database).

I just noticed, though, there's an error being displayed:
Warning line 187: preg_match() [function.preg-match]: Empty regular expression

The regex for the guild in question is set as: "/Alt of ([\w]+)/i" which has worked fine for as long as I can remember.

Let me know if I can provide any logs or anything that might help.

This might be due to a problem in the way the original per-guild config is set up. Once you open per-guild config for a guild, a guild-specific config is created and can't be turned off again.
This has been fixed and there's an on/off button in the latest SVN. Can you please update to that, and then check if all of the per-guild configs are either set up correctly or turned off?

Using 1540, I have no menus to change settings. Firefox is reporting a javascript error:
subcontent has no proerties (tabcontent.js line 91)
subcontent.style.display=(subcontent.id==subcontentid)? "block" : "none"

I am not seeing this error in my firefox. Are you getting this on /rostercp/addon/memberslist.html ?