Slic3r/pronterface starting at wrong z height

This problem seems only to happen with certain files, so I don't know what the problem is. Here's what happens:
I load a standard file, say, the full-tray Prusa file for reprap parts. It goes through Slic3r. Seems OK, but when I go to look at the first print layer it seems to be up a few mm from where it should start. It is as if the Z of the file was below the print bed's Z level. However I check the file in any number of 3d drafting programs and it is indeed Z-correct, I try re-saving it but the same problem continues to happen.
If I use other individual files even from the same author, no problems, prints happen just fine.
The printer itself is following instructions correctly, because it prints just what Slic3r and Pronterface are telling it to do: print the file with the very bottom few mm's (maybe 5mm or so?) offset/chopped off.
Using MacPronterface and Slic3r 0.9.8
I have read somewhere that if z-retract is set, some goofiness happens with the first layer, but I have it set to 0.
Any ideas?

I had that in the beginning and found it rather strange!
What I do now is load a file but NOT click "print". Then, when temp is up to level, I home all axes manually , then click print. (They will home again) I have had no problems since but am still puzzled as to why it originally happened. BTW, I disabled (set to Zero) the temp setting in Slic3r and do them manually in Pronterface - it seems to start quicker that way.

The thing is, according to the processed g-code, the bottom 5mm does not exist-- the file starts printing at that chopped-off bottom point. So even if I home it again and print it again, it still prints a chopped-off job. I am thinking it is a problem with Slic3r.

Furthermore, it's doing weird things on other large-plate files such as shut down the temperature of the hot end and print bed at the beginning of the print, which it does not do on other smaller print jobs. Not sure what's going on here. I'd post the files here but they are too big.

Here's the tray which prints as if it's chopped off the bottom 5mm:
[mega.co.nz]

here's the one that prints right but kills the temp once it starts:
[mega.co.nz]

Well, strangely enough, both of those STL tray files have problems according to Nettfab and slic3r so maybe try and get alternative files. Dunno whether that has caused your problem though