We charge a nominal fee for prep on small gauge scanning (8mm and 16mm up to 2k): a few bucks per reel to cover the cost of the leader and the 5-10 minutes work it takes to actually make two splices and rewind the reel. Others charge more for this. We originally didn't charge anything for it, but leader can get expensive (especially when you have to prep 100+ 50' reels), so we charge for that now. In most cases, this is all we need to do, because our scanner can deal with most bad splices or perf damage, so prep time is pretty minimal. On scanners that can't deal with bad perfs, there may be more setup involved, so they may just charge a larger flat rate for everyone.
We don't charge for file copying. You're paying for digital files, and the only way to get them to you is on a hard drive or similar media. Charging for copy time is a little nickle-and-dimey feeling (though at the rates you quote, that's a lot of nickles and dimes). That said, if you absolutely had to have files right away, we'd charge a rush fee for a large file copy operation - it ties up the machine and we can't be scanning on it at the same time, which costs us money. In most cases, with large file copies, we just set it up to run overnight when it doesn't matter, and we don't charge for that.
(By the way, Firewire is relatively slow, especially for large files - eSATA would be much faster, and is what we recommend/prefer for DPX/TIFF scans).
Depending on the scanner and workflow, there may be more or less work involved in any given operation from lab to lab. For example, our scanner can scan directly to ProRes file (or to DPX or TIFF or whatever). A lot of scanners only go to DPX or similar image-based formats. If you don't need DPX and just want a ProRes file, we just scan right to that format and we're done with it. With other scanners, you need to do a file conversion. That does take up computer time, plus a nominal amount of operator time to set up the job, but it's largely an unattended operation. From your perspective, you just want ProRes, so why should you have to pay for a conversion from another format (totally understandable point of view, I might add). But from the lab's perspective, the scanner doesn't do that, so there's a lot of work involved for them.
The pricing for this stuff can get complicated, which is part of the reason we don't put our rates on the web site. Sometimes that information is misleading and you can actually end up paying less (or more) than the rate sheet shows. Kind of like taking your car to the mechanic: they're not going to give you a price to fix something without figuring out exactly what they need to do first.
My feeling is that charging a lot for things that don't involve skills (copying files, for instance) isn't in our best interest, so we don't do it. Then again, our overhead is much lower than many other labs, and we're not in LA, where apparently you can charge for things like that.