Beeping in CM PBEM files seems to be a sign of data corruption during the transmisson via the internet. It is an unfortunately a not uncommon problem with PBEM files. It can render the whole file unreadable. Always keep copies of outgoing PBEM files until you are sure that your opponent could read them. Sometimes the problems can be fixed by your partner resending the file. Another suggestion is that your partner checks the encoding mechanism of his/her email software. Maybe it is encoding in a weird format. If that is the case, ask them to change to MIME or Base 64.
When receiving PBEMs on a Mac, I usually just drag them from the attachment window in Eudora (works with any other mail software like this, too) to my desktop, open CM and then load them from there. Normally I don't have problems.
If you have Stuffit 5.x (freeware from e.g. www.aladdinsys.com), you can unzip files from Windoze Zip format. Zipping them is a reasonably good protection against code degrading. Remember that Windoze users usually can not unstuff files you protect like this. You can zip files using Shareware you will find at www.download.com or www.tucows.com So if your partner zips the file, you would drag it to your desktop, wait a second until it appears, then drag the icon onto the alias for Stuffit, and the PBEM file will appear on your desktop.
The last possibility is that your partner is opening the file in a word processor, e.g. Word, selects all, copies and pastes the selection into the body of the mail message. The file states clearly where the data starts and ends. All you have to do is to copy it from the email body to a word processor (SimpleText won't work. b/c most of the time the files are too large), save it and open CM, load the file. That does not work for me on Yahoo mail, but it did work for two people I advised.
Final point, units refusing to take orders. Sometimes tanks will not take orders in a PBEM game. When trying to give orders all you get is a beep. If that happens, abandon the turn and reload the PBEM file. 99% of the time this will fix the problem.