Binded xrefs all blocks are mirrored/rotated
Are you using the INSERT method to bind the external references?
For the blocks that are being mirrored and/or rotated: are these blocks present in multiple external references -OR- are they defined in the host drawing as well as in at least one external reference?
If both of the above are true, are the block definitions for these blocks inconsistent in the various drawings in which they occur?
One way to get the effect you are seeing is to have a block definitions using the same name present in multiple files (host and/or externally references) but not having the same definition in each file. Perhaps the basic graphics are the same, but relative to the insertion point, those graphics are mirrored, rotated or both. When you bind using the INSERT method, the file name prefix is stripped, leaving just the block name. The first definition in the bound file (the host file definition, if present; otherwise, the first external reference with the block definition to be bound) "wins". Any bind operations occuring later will use that first definition in lieu of the one in the file being bound. If all the block definitions are identical, there is no problem. But if they are different, then the result for the files bound later will be a change to what the source files show.
The "easy" way out is to bind using the BIND method. This will prefix the named objects in the file being bound with a string including the external reference name, keeping each definition just as it was in the source file. But that will affect all named objects, not just block definitions, so you will likely end up with multiple versions of layers, linetypes, dimension styles, text styles, etc.
The "hard" way would be to make a list of all of the affected Block Definitions, determine the "correct" version of each, update all the files with the correct block defintion, check each instance of each corrected block definition in the files and rotate and/or mirror each one to get the original orientation of that block in that file and then bind the drawings using the INSERT method.
