Problems using ncread with some variable names

I'm using ncread with a file containing variables with simple names (e.g., Tair), but others with very long names with '.' separating parts of the name (e.g., MODIS.MOD15A2.MODFpar_1km_QA1.values). Those "long" name variables are completely ignored by ncread, not displayed by ncinfo and of course a message error if you try to read them. However, I do not have any problem reading the long name variable value with other nc tools, such as ncdump, Panoply, etc. As a workaround I build an mscript to dump the values with ncdump to an ascii file and then reading the ascci file in matlab. I was wondering if someone had experienced similar problems and found a nicer solution that dumping the value with an external function outside matlab.