You mentioned you upgraded your O/S from htc ??? If you have done that all your added 3rd party software is deleted. Garmin is 3rd party and does not come builtin . Most probably your seller added in to you as a "gift". So to get it working, you need reinstall it

For flashing - check out these at http://forum.xda-developers.com RHODIUM section. Please follow instructions carefully or you end up with a expensive paperweight. Flashing is for those who wants the faster or latest firmware. Example my unit is now on Windows Mobile 6.5 Manila 2.1 - these are not official released by Microsoft yet and will appear in the new PDAs scheduled released this mid Oct. Anyway TP2 users will get a free upgrade. However if you have hflashed your unit to the umofficial one, you will need to reflash it back first to remove the HardSPL IDs ( learn aall these from XDA )

Alarm issue - RARE ; why don't you check your alarm files - maybe is not there as probably again the file you have chosen is a added file not builtin by htc. Just go to Systems/Sounds and Notifications to check and select a new alert file