I did some code inspection and numerous tests on this today and unfortunately haven't come up with anything yet.
Here's a filter file you can try: (note these are all in the reserved documentation range 2001:db8::/32)
testrange1:2001:db8::5-2001:db8::9
testrange2:2001:db8::5:1234-2001:db8::9:1234
testrange3:2001:db8::5:1234:1234-2001:db8::9:1234:1234
testrange4:2001:db8::5:1234:1234:1234-2001:db8::9:1234:1234:1234
testrange5:2001:db8::5:1234:1234:1234:1234-2001:db8::9:1234:1234:1234:1234
testrange6:2001:db8:1234::5-2001:db8:1234::9
testrange7:2001:db8:1234:1234::5-2001:db8:1234:1234::9
testrange8:2001:db8:1234:1234:1234::5-2001:db8:1234:1234:1234::9
testrange9:2001:db8:1234:1234:1234:1234::5-2001:db8:1234:1234:1234:1234::9
Just save that to testfilter.txt on your desktop and load it into the Tixati filter. It should say 13 /64s are touched.
Then, create a new channel (just name it randomly) and try to add some peers from the chat tab:
/addpeer 2001:db8::7:55555
/addpeer 2001:db8::7:1234:55555
/addpeer 2001:db8::7:1234:1234:55555
/addpeer 2001:db8::7:1234:1234:1234:55555
/addpeer 2001:db8::7:1234:1234:1234:1234:55555
/addpeer 2001:db8:1234::7:55555
/addpeer 2001:db8:1234:1234::7:55555
/addpeer 2001:db8:1234:1234:1234::7:55555
/addpeer 2001:db8:1234:1234:1234:1234::7:55555
They all come up in the connections tab as 'IP Filtered' for me, on Linux and Win7.
The IP filter parser trims the label, then takes what is on either side of the hyphen and puts it through the same generic IP parser routine that is used everywhere else in the program, which generally forwards those calls to WSAStringToAddress on Windows or inet_pton on Linux.
Perhaps in your case(s) there is something in the label or address that I am not catching with these tests. If you can formulate a test case that fails, please don't hesitate to post the exact lines here. Replies will now go into the mod queue first, so it will only be visible to you and us until a mod has a chance to clip out any real IPs and forward the original message to me.
If there is indeed a problem here, I'll probably be able to get a quick fix into the next release (soon).