To sort of close this thread to an extend:
It seems that LaTeX requires the file paths appearing in the \input or \include commands to be relative to the master file (anyone knows if there is a command in LaTeX to change this behavior?), regardless of which file they are included in (this really only applies to nested inputed files).
The drag command in the bundle now attempts to locate this master file and create such a relative path.
Further, if you keep the option button pressed when dragging, \input is inserted instead of \include.
Haris Skiadas Department of Mathematics and Computer Science Hanover College