Ok, here's a wonderful link about clover and the issues that are potentially associated with it: http://www.extension.umn.edu/gardeni.../Clover_FS.pdf
It seems that the issue with the red clover is that it takes longer to dry, and thus is more prone to mold. All of these issues are associated with mold being present on the clover, not the clover itself.
I do have to say that after reading this I would not be too keen to try new hay with clover. However, if you already know that your horse is fine with these bales, I see no reason not to feed them unless they seem inconsistantly dried to you.