No problems here, and since it doesn't work at commandline, it can't be caused by a corrupted popups.ini
The only reasons I can think of offhand for not being able to OP someone, is that:
1. You're trying to ask chanserv to do it, and chanserv doesn't recognize you as authorized to do it.
2. Someone has enabled the nickserv open to reject being opped by anyone.
3. You're not actually an OP.
If there are any status window error messages caused by trying to OP someone, that would provide a helpful clue.