Please try to vacuum/analyze and reindex your database - http://hm2faq.holdemmanager.com/questions/5/Database+Manager+(Ribbon)#maintenance
If you continue to have problems, try the following:
Try creating a new DataBase and import a small portion of your \HM2Archive so you can see if the problem exists in the new DB - http://hm2faq.holdemmanager.com/questions/3091/How+to+create+a+new+database+and+import+previously+played+hands
If the new database seems to work properly, it sounds like your database might be corrupt. Please continue to use the new database and import the rest of your hands using the steps above. This is why regular backups are a good idea. If your database becomes corrupt you can restore a backup and only have to import the most recent hands (that were played after the backup was created) and edit any tournament results if necessary. I recommend keeping at least the most recent 2 or 3 backups in case the most recent one does not restore properly you can try the previous backup.
If you continue to have problems, please reproduce the problem and zip/attach your HM2Logs folder with a detailed description of what you were doing and what problems you were experiencing - http://hm2faq.holdemmanager.com/questions/1921/How+Do+I+Send+a+Log+File+to+Holdem+Manager+Support%3F