I beat the game and am playing on 5 star difficulty in Challenge Mode. The problem is that my bolt multiplier keeps resetting even when I don't take ANY damage at all. Is there a glitch in the game? The resets seem to be somewhat random to me.

i dont know whats happening but i have read in the cheat section that it resets if you walk through a holoshield launched from the holoshield launcher (the ones you fire, not those that come up from the ground at some places)

If you have finished the game on exterminator than keep going until you have finished it as much as you want finish 100% for bragging rights then just start again and if it still resets at random intervals than it'll just take a little longer to buy stuff.