Ok, given them all a pretty thorough testing with that huge model, and well...it doesn't look too great.

In this model there are sixty 3840 poly spheres arrayed around a parent object - a cube. All the sphere's are set up as separate subobjects of that cube.
COB scale factor in all programs was 1.00.
Each test involved opening from the SCN and then saving as POF, closing and reopening PCS2 to get the in PCS2 results, then going in-game to get the in game results.
Here's the source SCN file these came out of:
http://sectorgame.com/ti-file-dump/VasudanAdmiral/test2.zip (copy & paste link)
====PCS1:======Model Comments:==
Input was: 61 Materials, 61 Groups, 64 Lights, and 61 PolyGroups.
Started with 115328 and ended with 115328 points, in 230412 and 230412 faces respectively. Compile time was 228.656000 seconds.
==Results:==
In PCS2:
- Correctly displayed
-
BSP debug mesh- 61Mb POF file
In game:
- Consistant 47FPS (though it was slowly dropping, I suspect a memory leak in FS there)
- Fully collidable mesh
- All visible polys were shootable
- No holes
====PCS2 Normal Build======Model Comments:==
PMFSaveToPOF: Compiled on PCS 2.0 Beta with PCS 2.0 Compiler Version 1 RC2
max BSP depth was 22
most polys in a single node was 1
==Results:==
In PCS2:
- Incorrectly displayed - massive holes all over model.
("Holy Snowballs Batman!!")-
BSP debug mesh- 42Mb POF file (probably smaller due to massive holes)
In game:
- Consistant 47FPS again
- Nothing but the cube in the centre was collidable
- All visible polys were shootable
- Huge holes visible in PCS2 are also present in-game
====PCS2 BSPEX Build======Model Comments:==
PMFSaveToPOF: Compiled on PCS 2.0 Beta with PCS 2.0 Compiler Version 1 RC2
max BSP depth was 16
most polys in a single node was 1
==Results:==
In PCS2:
- Incorrectly displayed - massive holes all over model again
-
BSP debug mesh (looks leaner)- 38Mb POF file
In game:
- Consistant 45FPS
- Nothing but the cube in the centre was collidable
- All visible polys were shootable
- Huge holes visible in PCS2 are also present in-game
====PCS2 BSPEX2 Build======Model Comments:==
PMFSaveToPOF: Compiled on PCS 2.0 Beta with PCS 2.0 Compiler Version 1 RC2
max BSP depth was 16
most polys in a single node was 1
==Results:==
In PCS2:
- Incorrectly displayed - massive holes all over model again
-
BSP debug mesh (almost same as previous)- 38Mb POF file
In game:
- Consistant 44FPS
- Nothing but the cube in the centre was collidable
- All visible polys were shootable
- Huge holes visible in PCS2 are also present in-game