Is there any way to make fvwm pager not see itself, so that its box doesn’t show up in the pager? I’m trying to make it look like part of my background, and that kinda ruins the feel of it. 
Putting the line Style FvwmPager WindowSkipList in your config will fix that. The WindowSkipList style command stops a window showing up in several places, like this and the window list.
Try:
Style FvwmPager WindowListSkipand in your FvwmPager config:
*FvwmPager: UseSkipListDoh! Thanky 