hi
i agree with tkchiu. While working with assembly in V5 just completely forget about using 'save' or 'save as', it is fatal!!
The option 'save managament' gives you a freedom of not only what to save, it also gives asks you where you want to save the parts and sub assembly files. This option...
well, i feel the only solution to the problem is to create some features (on IGES parts) used in assembly like axis, face etc. These artificially created entities can be used to give assembly constraints
Regards
jantu