Flash drive only "pretends" to eject - help!

I am trying to transfer data from a Power Mac G5 running OS 10.3.9 to a 4 GB USB flash drive. After finishing the copying procedures, I attempt to eject the drive by dragging it to the trash bin, clicking the eject button within a finder window, or using the "eject" option from a pull-down menu, etc. The drive icon disappears from my desktop, but somehow it has not "finished" ejecting, for when I pull out the drive, I get the error message about not having ejected properly. I've tried this multiple times, even waiting for several hours for the ejection process to "finish," and each time have ended up with at least 1/2 my files on the flash drive being corrupted and useless.
I have a large amount of data to transfer, since I'm trying to get it transferred from an old work/school computer to a personal computer at my new workplace. Thus, for efficiency's sake I cannot spend days/weeks transferring these data in smaller bits and it's not worth trying to go through the hundreds of different files to check each and every one to see if it's been corrupted!
Any suggestions? Thank you!!

Thanks for your help so far, BDAqua, Squirrel2 and Japamac.
The only Mac I'm working with is actually this one here at school - the other computers at home and my new workplace are PCs running Windows XP and 7, so I guess reformatting the flash drive in HFS+ is out. The ultimate place I'd like to get the data stored is an external hard drive, but it of course has an NTFS filesystem, which a Mac can't write to... and the work-around I found (NTFS-3G for Mac OS X plus MacFuse) only works with 10.4 and up.
When copying using the flash drive, I've always been connecting it to the direct ports on the towers (whether the G5 or my PC)
We can't upgrade the OS due to software incompatibility/price issues, so I'm kind of stuck with it - argh! To add to that, I'm wary of running troubleshooting or drive maintenance on the G5 right now since it contains data and programs belonging to a number of other people, and it's not feasible just now to run the risk of letting it go out of commission, even for a day (it's thesis-writing season!). That said, I'd be willing to bet a good bit of money that the G5's hard drive is not in "good health," so I'm just going to try burning my data to a DVD so I can be done with this machine once and for all! I've had some issues in the past with writing DVDs on this G5, but it appears to be my last chance unless I'm willing to wait a while.
A friend of mine suggested using Dropbox, which I was very gleeful about until finding out that Dropbox only works on 10.4 and up, as well!
Anyway, thanks again for all of your help and suggestions!

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Thanks Siva Aadhi-CIT. MCITP

Flash drive only "pretends" to eject - help!

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