How to solve compatibility issue with VMS-generated .MAT files (v5) and current 8.1?

Background:

Our current VMS system generates .MAT(v5.0) files from thousands of collected data points. They are transferred via FTP to a PC (Win 2000) set up specifically for MATLAB 6.5. Everything has worked great for 11+ years.

I am in the midst of upgrading our 6.5 version of MATLAB to 8.1 (on a Windows 2008 Server R2 machine, 32 or 64 bit). When testing the .MAT files, the current version cannot read them. I get the "File may be corrupt" message. I've re-saved the .MAT files in various versions( -v6, -v7, -v7.3), allowing the .MAT files to be read in, however, the data that is displayed in the workspace is completely inaccurate, breaking all of the M-File graphing scripts.

The M-Files from the old system seem to run great on the upgraded MATLAB version, give or take a few function name changes/syntax.

I checked to make sure the files were still binary .MAT files when brought to the new machine, so that's not the issue.

I've ran the utility program MATCAT (which checks for corrupt files) on all of the .MAT files that I converted from v5 to v6+. The script tells me everything is OK and lists all the variables and their sizes (not accurate). The funny thing is when I run MATCAT on the old system, where everything is working fine, it tells me every file is corrupt.

Issue:

It boils down to needing the capability of reading the v5 .MAT file data generated on the old VMS system accurately into MATLAB 8.1. The M-Files cannot do their job since the .MAT files it pulls variables and data from aren't correct and are hardly readable by 8.1.

Question

Do I need to reconfigure how the VMS system generates the .MAT files in order for them to be accurately read into the new version of MATLAB??