I would be very surprised if that were the case because I have run these types of simulations before with multiple Matlab files and they have worked for me. If that were the case then the InputPort1 variable would be overwritten, but it should be overwritten with at least the same number of samples, unless of course one of the m files is increasing the number of samples somehow.
Have you tried using both m files as individual components and see if one of them doubles the samples?
Regards