I have seen several occasions where BigFix considers a system to need rebooting almost immediately after logging in after a reboot!
Usually this is because of a windows patch, not BigFix itself.
There are two registry keys BigFix uses to determine if a boot is needed, one due to BigFix and one due to Windows.
The above link should give you a lot more insight into this. I have used the second registry key to determine what the system was needing the do and either manually did it or cleared the key a few times to get systems to stop the cycle of rebooting.
I also discovered that if you have a baseline with a lot of fixlets in it, as soon as the first fixlet sets the ‘reboot pending’ flag, the countdown begins if you use the “Reboot Pending” fixlet as a policy to auto-boot systems - Not good - I had to stop doing this just due to this issue.
Currently I just have three policies per baseline, one for users, one for testing, and one for critical systems. Users reboot after 1 day, critical never reboots but the request stays on top, and testing reboots 30 minutes after the baseline completes.