What kinds of computers are you using?
Certain version of MySQL build different forms of tables on different machine architectures.
My ears perked up when you said some records were empty because that's what I had when I tried to bring data from my PowerPC G3 chip PowerBook (running LinuxPPC) to my Intel P-II Linux box.
I have a vague memory of the problem being something to do with myisam (sp?) table formation or something like that.
There ought to be a way, however, to suck your data down to a lump of insert statements and insert them all on the other box.
Let me know if you find a fix!
-john