I've owned four Baby Eagles over the years, the full and semi-compact 9x19mm, the full-size .40, and the .45 (available in semi-compact only).
All four pistols preferred Mec-Gar magazines. Factory magazines may in fact be Mec-Gars; the only time I ordered a "factory" magazine I went through a dealer and I ended up with a Mec-Gar. The only problem was with the .40, in that two of the three mags wouldn't always lock the slide open on when empty.
The 9x19mm magazines also had a very annoying rattle when loaded to capacity, worse than any other pistol mag I've encountered, including S&W 5906 and Kel-Tec mags. With one in the pistol and one in a pouch at my 9 O'Clock, I sounded like a cowboy wearing riding spurs.
All three calibers shot well, but I had the best experience with the .45. I think the Baby Eagle in .45 is a "sleeper," although the prices I've seen at dealers lately may indicate that the popularity of the brand is increasing ($579 new).