I has BRL-CAD 7.0 installed on my machine, and a co-worker of mine pointed out an issue with RTCHECK. After the command was executed, the command window reported "0 overlaps", but if you switched views in the graphics window, it showed the overlaps color shading on my model. To my dismay, when I loaded the model on a pre-7.x version of BRL-CAD, the command window reported several dozen overlaps...which agreed with the overlaps shown by the graphics window. I recently installed BRL-CAD 7.2 and it seems to have the same issue...the command window reports 0 overlaps while the grahics window highlights the apparent overlaps. Has anyone else seen this same issue?
This has been recently reported (within just a few days actually). Are you running 7.2.4 or a previous version? I suspect even the latest exhibits the problem, though I've been unable to reproduce the problem locally. Would you provide a simple example geometry and views that show the problem? You can submit it to here https://sourceforge.net/tracker/?group_id=105292&atid=640802
If it's the bug that I have in mind, it's a problem with the multiprocessor handling of rtcheck. If you limit rtcheck to a single CPU, it should work. That is, use rtcheck -P1 to request that it only use one cpu. It will take long to run depending on how many CPUs you have, but it should return the overlaps correctly -- that is, assuming it is indeed the same bug. If it is, this may be fixed in the latest posted release (need testers).