if you have a signature that is just under the 100 char limit, and contains a url using [ url ], I.e mine is:
-- codemastr
[ url ]http://www.unrealircd.com[/ url ]
[ url ][url=irc://irc.axenet.org][url=irc://irc.axenet.org][url=irc://irc.axenet.org]irc://irc.axenet.org[/url][/url][/url][/ url ]

Next time I go to my profile, it reads:
-- codemastr
[ url=http://www.unrealircd.org ]http://www.unrealircd.com[/ url ]
[ url=irc://irc.axenet.org ][url=irc://irc.axenet.org][url=irc://irc.axenet.org][url=irc://irc.axenet.org]irc://irc.axenet.org[/url][/url][/url][/ url ]
Which is now over the limit and therefore I have to manually modify it each time I edit my profile...

(spaces were added so the forum doesn't replace it with HTML tags)

Yep, noticed that too.
Everytime when i change my profile, i have to change it back to the [ url=http://..>..[ /url ] format instead of [ url=http://... ][ /url ]

Yup, and when I enlarge the allowed signature size people will add more info to it and still have the same question.... Sorry, I hope you understand I'm not going to make the sig size larger.

That's not what he meant.
Example:
First i make a signature with the url tag.
At the moment i'm creating it, it is within the limit.

Then later I go back to my profile and the forum has automatically changed the url tag making the sig exceed the limit, so everytime I have to change the format back before I can make any change whatsoever to my profile.

Yupyup, I perfectly understood that :-)

Well I'm not asking you to expand the signature size, I'm saying you should contact the author and tell them there is a bug, if I understand the software you are using is not free, and therefore the author should look into problems you report.

For coders:

The solution would be to not store the expended version, but instead store the original version and expend it when it's time to display the signature, before it's translated to HTML. (Even better, save some cycles and don't expand it at all, translate to HTML directly.)