Hello Alberto,
Are you calling MATLAB via ActiveX? According to KnowledgeBase 2A6E3SDM, which I linked below, MATLAB's ActiveX interface looks like version 5.3 but has all of the capabilities of version 6.x, if you have both versions installed. If this is the case, it looks like this was the intended behavior and there is not a way to change the UI, because of the way the ActiveX interface was configured for MATLAB.
I hope this helps!
Incorrect MATLAB Window Appearance when Called from LabVIEW
http://digital.ni.com/public.nsf/websearch/21F5F9E84FC1EAFC86256A64006E6570?OpenDocument
Liz Fausak
National Instruments