Pain in the backside bug. Help anyone?
 

I am having trouble with a map I am trying to create.
I have been testing versions as they progress in Single Player mode and everything has been fine.
Recently I felt that it was ready for beta testing with actual people and so I got rid of my Single Player Start marker, switched the map type to TDM, added some Red Team and Blue Team Markers and saved.
I also set up a TKOTH version.
So I now have three versions.

A single Player version with a single player start point (for testing)
A TDM version with one red and one blue start point.
A TKOTH version with one red and one blue start point.

The start points and the game type selections (in Level Properties) are the only things that differ.

Now then, when I reload the TDM and TKOTH maps back into NILE I get a message that some blocks were not processed and to Please check installation before editing.

Now I can continue editing the Single Player version all I like it is only after I remove the player start, switch game type to TDM or TKOTH and add the team starts that this problem occurs.

In-Game the TDM appears to work fine but TKOTH crashes to desktop everytime (no crash in NILE just the initial error message) before it even attempts to load up.

It makes no difference how I approach it either. I have deleted the TKOTH and TDM versions and converted from the Single Player map a few times. I can add to the single player version and no problems. Its just when I tell NILE its a team game that things go funny.
I have made simple tkoth and tdm maps (ie one player start each side and a zone on a terrain and nothing more) and everything works fine, in game and in NILE.

It makes no difference if I save as NPJ or NPZ either.
Its a weird bug and I cant for the life of me work it out.