Not entirely sure how to reply to the mailing list via email, hopefully this will work...

Subject: 
[TxMt] Re: Disabling entire bundles doesnt persist
From: "Allan Odgaard" <mailinglist@textmate.org>

> When you disable the item and save, TextMate should create the following file:
>    ~/Library/Application Support/Avian/Bundles/AppleScript.tmbundle/info.plist
> Does that file appear on your disk?

Hm, I just noticed what was actually happening is instead of updating AppleScript bundle, it was silently creating a new AppleScript 2.tmbundle, AppleScript 3.tmbundle etc.

> Additionally it updates the index, which is located at:
>    ~/Library/Caches/com.macromates.TextMate/BundlesIndex.binary
> You can check the date of that file. You can also try to quit TextMate, remove the index, and then relaunch, that will make TM generate a new index.

Thanks, this fixed my problem. 
I deleted the index and when TM relaunched, the unwanted bundles are hidden and disabled in Bundle editor.

I guess it somehow got out of sync