I have the very same problem.
I presume it is a problem of Matlab r2009b for the first time using the newer libiomp5.so OMP shared library, COMSOL 3.5a still using the deprecated libguide.so OMP shared library. Unfortunately I cannot check right now. I suggest trying Matlab r2009a (with Hotfix1 applied to COMSOL 3.5a), which still uses libguide.so (COMSOL support just mentions that Hotfix1 is compatible with Matlab r2008b aund 2009a, no mention of r2009b).
Regards
Rumen
I presume it is a problem of Matlab r2009b for the first time using the newer libiomp5.so OMP shared library, COMSOL 3.5a still using the deprecated libguide.so OMP shared library. Unfortunately I cannot check right now. I suggest trying Matlab r2009a (with Hotfix1 applied to COMSOL 3.5a), which still uses libguide.so (COMSOL support just mentions that Hotfix1 is compatible with Matlab r2008b aund 2009a, no mention of r2009b).
Regards
Rumen