It sounds like this depends on the way the CSS files were concatenated. This was not specified, but I tested with files that are UTF-8 encoded with BOM (as produced e.g. by Notepad when saving as UTF-8). If such files are concatenated using a method that simply concatenates the byte sequences, this means that the BOM U+FEFF appears within the result file too, not just at the beginning. This makes it appear between CSS rules, causing a syntax error (which should be reported by the W3C CSS Validator, but maybe the error message was not noticed amongst the warnings). In browsers, this syntax error seems to cause the next CSS rule to be ignored.
So this is conjectural, but if the rules appearing at the start of some of the original CSS files are essential to IE rendering but not on other browsers, then the symptoms would be understandable. The solution then would of course be to concatenate the files without BOM.