Hmmm, that does not sound exactly the same as what I had actually. The colours can cause problems during the MIMAGE procedure, since the converter will start finding non-existing ID's (will prevent ever updating of eu2map file till fixed). That was the case especially with older versions of magellan, until Inferis applied a less strict converter which fixed most such problems automatically. What it did not fix I had to recolour manually (in the id-map obviously).
However, if the eu2map itself causes problems when injecting the map, the usual errors can be twofold (in my experience)
-the regionlimit problem (prevents injection)
-the borderlayer-touches-PTI problem (causes CTD in game when moving near the area's affected). Borders may not at all cover any PTI-area. Which can be annoying since already in standard game they sometimes did. SImple fix is removing these.
A possible 3rd problem might be when mimage calculates the adjacenties wrongly, which it tends to do sometimes around rivers, which results in 'white stripes' in mview. Dunno the effect ingame of these, but I rather fix it asap before trying, simply by slightly updating the area in id and mimage again so it will recalculate the adjacenties.
Well, I posted my solutions to the most common problems I had, still not knowing exactly what problems you experienced, most of that might be of no use to you though
