Thinking maybe you're not getting them in all the way? They're going to be tighter then heck with the extra material sprayed on the bed-had to move mine around to different holes to get them all to go back in.
Yea, they're not going to fit anymore. If the sprayer was good, you have at least 1/8" of liner on the holes sides, making the effective hole 1/4" smaller all around. Plugs will have a hard time fitting and staying in.
The factory spray in bedliner is thinner, may adjust for the areas of the plugs, etc. However, there is a thread somewhere that talks about two different part numbers for the plugs, one without spray in bedliner, one with the spray in bedliner. I couldn't find it quickly. This thread discusses a modification to the plugs to allow them to fit.