are there problems with Prius's when they are not started for a long period of time ??I just looked at one that hadnt been started in a couple weeks and it needed to be boosted...

Dear Wes-- The problem you find could be true of any car, not just the Prius. The starting problem comes from the conventional battery and the gasoline engine only. The large battery pack under and behind your rear seat has nothing to do with starting the car. Good luck from Bovan.

I used to work at a Toyota dealership and we would have both the new and used Prius sitting on the lot for weeks and they would start up without any problem, and thats in the Northeast where the temp gets extremely cold in the winter.

The 12v "starter" battery in the '04+ Prius is pretty small...similar to one on a motor cycle. If your Prius is equipt with the smart key system (sks) and it is left on it's possible to drain the small 12v battery after 2-3 weeks..though others have reported no issues after as long as a month of leaving it unused. If you will be leaving the Prius for more than 2 weeks there are a few things you can/should do. 1)Turn off the SKS. 2)consider a small solar charger...a tiny 5W solar panel connected directly to the 12v battery will maintain its charge while you're away (can't use the 12v outlets as they are disconnected when the vehicle is off...to prevent 12v drain). 3)Consider a float or trickle charger if it'll be parked somewhere you can plug in. 4)If it will be along time away consider leaving the fob with a friend/neighbor and have them start the car and/or drive it around for about 20 minutes or so...the 12v is charged via the HV battery, but the car must be in ready mode for that charging to occur. Worst case scenario is that you need a jump start...it jumps similar to any other conventional vehicle except that the battery is in the hatch but you use a jump point under the hood (see your owner's manual or http://www.cleanmpg.com/forums/showthread.php?t=3750 When I park my Prius at an airport for more than a week I keep one of the portable jump starter/air pumps in the hatch just in case I need to add air to a tire or do an emergency jump...note that I've never had my battery drain or needed to jump my Prius in 3 1/2 years of ownership and I've left it un-started for up to 2 weeks at a time.

Your Aux battery is NOT the issue. Long term (2 months or more) the Main battery depletes and may need to be removed to be charged - Or Replaced.