I recently did some research on the version variable in gpt.ini, what it means, and how to modify it.  Unfortunately I found some discrepancies:

http://technet2.microsoft.com/windowsserver/en/technologies/featured/gp/faq.mspx says to increase the value by one.
http://technet2.microsoft.com/windowsserver/en/library/824b4758-9430-4633-8d8f-3dad0f2bf8391033.mspx says its an encoded representation of the user and machine settings versions
http://support.microsoft.com/kb/324800 says to add a 0 to the end or 1 to the beginning
http://www.microsoft.com/technet/technetmag/issues/2008/01/GPPerf/default.aspx?pr=blog says the number just has to be different, bigger or smaller

So what's the real answer?  The Group Policy Team Blog has a post on Understanding the GPO version number which basically states the same as the second article above, but goes into much more detail.  An excellent post; a must-read for anyone working with group policy.