It is not unusual for the vacumm to rise when you valve off the vacuum pump. This is because of the oil in the comp. The oil absorbs the refirgerant. When under vacuum the refrigerant is able to come out of solution and enter the system that is under vacuum, thus raising the micron reading.

Now you are making me get my "refrigeration Geek" on. It would take months of vacuum and heat to get all the refrigerant out of the oil. Since the vacuum only is present at the top most layer of the oil, the refrigerant trapped in the oil at the bottom layer has to work its way to the top layer by diffusion. It migrates very slowly. Some ways to help this along is to agitate the oil mix, shake the comp, bang on it with rubber mallet, etc... "geek" off.

In a system that has had refrigerant in it before, take the vacuum down to less than 200 microns. Valve off the vacuum pump. Wait to see what the micron reading is after 20 minutes. If it is 400 microns or below you are good to go. If it is above 400 then vacuum somemore.