3D shape missing holes

[Dr Dan]

Hi all, this is a 3D shape I built in MAYA. It's actually a liver sinusoid so approximately 15 microns in size! The half-pipe down the middle (this is where the blood will flow down) has tiny holes in it which are surround by a torus. These holes are present in Maya and also (when I export this) in photoshop where they can be seen as small black circles with surrounding red.

In photoshop the holes in the halfpipe are clearly present

HOWEVER, most of them have then dissapeared when I open them in Element 3D (the circles are now green which is colour of half-pipe)

In Element 3D the holes are now (mostly) filled in)

Any ideas why would be greatly appreciated.