Hello. We are aware of this issue – and we are currently working on fixing it.
For a temporary solution you can use cheats to skip the boss fights
Taken from official forum which no longer exists:
" 1. What are the cheats for DNMP?
Open the console by pressing the '~' key, then type
exec cheats.cfg
press '~' to close the console.
This will enable cheats permanently on DNMP, and void your warranty. Little joke there. There is no warranty. Seriously though, We do not support enabling cheats.
You then can press the following keys during gameplay:
'~' - open command line console
G - give all guns, ammo, babe, key
H - give all ammo
J - give jetpack
F - give forcefield
L - give extra-life
K - kill self
I - toggle invincibility
P - developer's pause (allows you to zoom through map)
'-' - small HUD
'=' - normal HUD
M - toggle map name
You can also jump to specific levels and areas
First, open the console (press '~')
Then type in the following formula : 'map eXpY_aZ' , where X, Y, Z= Episode, Part, Area
So to get to Episode 01, part 02, area 03, you would type:
map e01p02_a03
Finally, close the console (press '~' again)
You can use the M key to get to know the map names, then jump to them at will. "

I'd like to point everybody having issues with Prism3d.exe error, that we fixed that problem.
Resil explained this here ->
Duke Nukem Manhattan Project FIX
Have fun
Grah

Yes - the old installer was replace with new one :)