Some of the dungeons aren't respawning enemies. Is this happening to anyone else. Thanks.

Many MQ based dungeons have encounter zones that are set to never reset.

There's a few radiant quests that also do this, notable Mistwatch, and southfridge.

Keep in mind also that re-entering a cell resets its respawn timer. So, for instance, if a cell is supposed to reset every 10 days and you re-enter that cell 9 days later, the timer is reset. It will now take a total of 19 days for your cell to respawn. If you continue to enter the cell every 9 days the cell will never respawn.

Thanks I thought that it might be something like that. I mistakenly thought it was a 3 day cycle though.

Maybe you mixed up Skyrim and Oblivion?
Nothing in Skyrim resets in 3 days (taken from uesp.net):

here are three different schedules that can be used for respawning a game location:

• Never. http://www.uesp.net/wiki/Category:Skyrim-Places-Safe are flagged as "Never Resets", which means that no matter how long you wait the contents are never altered. All containers in such locations are http://www.uesp.net/wiki/Skyrim:Containers#Safe_Locations for long-term storage. This setting only applies to interior areas; any exterior areas associated with a never-respawning dungeon will respawn after 10 days. Examples of the areas that don't respawn are the http://www.uesp.net/wiki/Skyrim:Houses that you can buy.
• 10 days (240 hours) of in-game time. This is the default time period used before a dungeon or any other game location respawns.
• 30 days (720 hours) of in-game time. This is the time period used if a dungeon has been http://www.uesp.net/wiki/Skyrim:Dungeons#Clearing.

For any area to respawn, you must not enter the area during the specified time period. Each time you enter the area, the respawn clock is reset. Conversely, you can intentionally re-enter an area frequently to prevent storage containers from resetting (although you run the risk of losing everything if you forget to return in time).

I truley hope not! I just set off on a crusade to shrink my save file.