Yesterday I examined some of these 1500 'bad' files. What they all have in common is that they were converted, mostly to ALAC, by Sound Studio 3, which must have done something that is incompatible with JRiver MC. For some of these files I tried ALAC -> ALAC using XLD, and this cured the problem. It would be great, though, if this incompatibility could be fixed in MC.
By the way, there is absolutely no issue with files converted by Sound Studio 4, the current version, back in the hands of Felt Tip. They work perfectly.