You're right, the Acer laptop BIOS has no options to speak of. Here's what I would do in your case:
Click Start, Run, and enter:
Click OK. That should open Computer Management. Under Storage, click Disk Management. Look for your hard drive. Is there unused space? I'm wondering if you still have that 40GB partition hidden somewhere, and are now using the leftover space. If this is the case, I'm not sure why Partition Magic wouldn't see it. There's a few ways to solve it, though.
Ensure that you have the latest BIOS for your laptop. If not, update it. Now double-check everything in Computer Management and Partition Magic. If that doesn't solve it, try checking the jumper settings on the new drive. Master mode is no jumper, slave mode is a jumper on the lower two pins, and cable select mode is a jumper on the upper two pins (instructions should also be printed on the hd label). Try all three modes to see if that changes anything.
If you have an external USB enclosure, or a laptop to desktop IDE adapter, or access to a different IDE laptop, I would hook the drive to an existing computer and see how it reads it, both normally and using Computer Management. If the drive will not format properly on your Acer, maybe the solution is as simple as reformatting it on an alternate one. Also, there is always the very slim chance that if this is a used disk, it has been modified or damaged in some way so that one of the platters are not functioning.
If #1 and #2 produce no results and #3 is not an option, try this, just to gather information- boot with an XP install CD (SP2 or SP3... SP1 has a 137GB limit, IIRC). Go into setup, as though starting everything fresh. When it shows the partition information, take note. Is there more than one? How large are they? Any unused space? As long as you cancel out or turn off your computer at this point, no changes will have been made, don't worry.
Good luck, let us know how it goes!