Hi Gorka,
Thanks for your posting. This is Labview 6.0.2 under Win2k, by the way. MATLAB is being called implicitly [I am not writing any code that starts it up], and I am not sure if it uses COM or ActiveX or DDE or some other mechanism. If I create a VI with a one-line MATLAB script in it and look at the error output, Labview says "Error occured while executing script. Error message from server: . in Untitled.vi" (Untitled.vi is my instrument.)
When MATLAB came out with its last major release, there was no interface problem with the Labview code. It's odd that 6.0 -> 6.1 is causing trouble.
Chris