I've been having similar problems with my new installation of LM 17 Mate. The system only accepts my xmodmap settings if I input them in the terminal, or if I use the sleep command as above.
I notice that the system also seems to revert my xmodmap settings if I tap the "windows" key. Either that, or when I do something else that I haven't been able to pin down. This can get really hairy, as I sometimes don't notice that I've accidentally reverted my xmodmap settings, and then caps lock, and then notice that caps lock is on, so I run the xmodmap script... only to find that I've turned off caps lock while I already had caps lock on, meaning that everything is caps locked and the only way to turn it off is to log out and back in.
Interestingly, the first time I hit the windows key, the LM start window appears, but then on second and subsequent uses, my correct xmodmap setting (â) kicks in.
It looks like something is telling the system to ignore or try to revert xmodmap settings, and I'm not sure what.
It would be nice if the keyboard settings in LM17 would allow for open-ended setting of key bindings. As it is, the drop-down radio buttons and the variety of choices are nice, but nowhere near all the possibilities I want. Also, my guess is that that program is the culprit in these xmodmap problems. I don't remember having seen those settings in previous versions of LM, and I didn't have these xmodmap reversion problems in previous versions.
New desktop: Linux Mint 17 | Mate 1.8.1 | i5 2500K CPU | 8 GB RAM | GTX 560 Ti | c. 1.6 TB HD ||| Netbook: Xubuntu 10.04 | AMD Dual-core 1.6 GHz | 2 GB RAM | 320 GB HD