No matter I click on "yes" or "no", the message come back right away and I have to kill the textpad and start again with "ignore updates" option before I can get any work done.
I would rather guess that there is a process running that accesses the files you are talking about without you knowing about it. I never had trouble with this feature.
Try filemon from sysinternals to see if anyone accesses the file in question.
If TextPad is the only process accessing the file and you still get the dialog box, than you should post this issue to helios support. Maybe you have a special file system configuration.
If you get spurious notifications that a file has been modified, try checking the option to "Ignore differences in modification times less than 2 seconds" on the File Preferences page. (MS Windows caches remote files and the cached copy can get out of sync with some Netware and Unix file systems.)