When you add your "usual DC3 mods" are you accidently changing the viewpoint? the default DC3 and Manfred's C-47 have totally different viewpoints. These are the entries I find in my config files.
DC3:
[Views]
eyepoint=12.75, -1.512, 3.217
C-47:
[Views]
// longitude/lateral/height
//eyepoint = -6.495, -1.512, 3.217 // initial version
//eyepoint = -6.495, -1.512, 1.650 // correct eyeheight, zero VIEW_DIR angle
eyepoint = -6.495, -1.512, 2.000 // keeping correct eyeheight, using VIEW_DIR 7 down
Add your repaints before your DC3 mods and see if the vc is still there. I'm thinking your mods are booting you out of the vc.