Okay. I went ahead and logged this issue as TT 3596.
Now, please realize that a likely response to this TT will be that Markus has not seen this behavior and cannot recreate it. We have informed him that this problem has occurred, but we have not fully explored the circumstances and settings which likely caused it. The waiver AI is fairly complex and unexpected results can occur when unusual combinations of settings and circumstances are applied.
I myself have spent many hours exploring this exact issue in early builds - waiver behavior with clean slate leagues. I can assure you that productive solutions are much less likely to be found when one merely states that a problem has happened and does not attempt to discover the exact circumstances in which that problem happened.
If you are interested in seeing this issue resolved, then yes it would potentially be useful to know if foreign players are prevented from joining active rosters in your league. Maybe the AI waives players from its 40-man roster who it knows will never be able to assist its major league team. Maybe the AI waives players who it tries to promote to the active roster and cannot due to such rules.
However, should you prefer, you could FTP your .dat files and let us know what you have named your file. Some information can be gathered from that method as well.
How to FTP Files to Us