have a look at the top of the mag, do the holes line up together, and are they the same size? Also put the working metal and the lowcap next to each other. check around the top. Make sure the distance between the top lip and the lug below match up. if they do not then you will find that the lowcap will sit in the mag well, but there will be a small extra gap at the top. You can shave this down using a knife/file. If you hold the mags together you will see the difference in the catch part of the magazine, this is the issue.
I had this with some mags on my cyma. Some fitted some didn't feed right. When companring the two I founf a definate square edge to the one that worked and an angled edge to the one that didn't, a file of about 1mm of plastic and they fitted and fired fine.