Hi,
I don't know what types of GBIC's you ar using, but there is a known problem with flapping links on some WS-G5483 (1000BaseT) GBIC's
Check the following bug-ID if you are using WS-G5483:
http://www.cisco.com/cgi-bin/Support/Bugtool/onebug.pl?bugid=CSCdx18452&cco_product=Catalyst+6000&fset=&swver=&keyw=GBIC&target=&train=
If you are using other GBIC's the problem is also more likely about bad connections instead of any software issue.
I had the same problem with a WS-G5484 on a 4506 chassis, replace the fiber optic cale and problems where solved.
Hope this helps and kind regards,
Leo