Actually, I used to run into that issue as well. To fix the problem, what I did was make a large Illustrator doc. To get the correct size I copied a character from an installed font (just pick Helvetica or something) and pasted it into Illustrator. It should be rather large. I sized my Illi document to fit and set up guides and such to kind of show x-heights and the like. Then I take whatever font I'm working on in Illustrator and I copy each character (or line of characters to keep sizes correct) and paste it into that new illi document. Then I scale everything up to the correct sizes. Once everything is all scaled I then can copy/paste into FontLab without crazy curve changes. And if it's set up correctly they should just be scaled to the right size that you want in FontLab. no extra scaling and whatnot.

It seems complicated at first but it's actually saved me HOURS of work. I can pump out fonts pretty quickly now with this method.

If you'd like further instruction or a walk-through then message or email me somehow. I think you can figure it out on your own though. It's simple enough.

You can save even more time by using ScanFont. It's advertised for its ability to autotrace scanned images, but it's most useful feature to me is the ability to go from an entire file of Illustrator outlines to a bunch of glyphs Fontlab in a few simple steps. I've gone through the process in under a minute in some cases.

You may find this video useful.