First off, I'm not going to deal with any jumpers besides those for determining master/slave. They're either not to be messed with or for limiting capacity on older systems. Neither should be involved with your problem.
As a rule, the master drive should go on the end (black) of a modern cable (blue/grey/black). Technically this should only matter if you're using Cable Select settings to determine master/slave, but specifications are not implementations. Some drives do not like having their CSEL pin floating when they're the master or grounded when they're the slave. It sometimes only causes a problem with certain disk controllers and not others. It's a black box problem unless you want to debug your particular devices. I can't guarantee it's contributing to your case but it been the problem several times for me. I'd switch it.
For Disk 1, the IBM, it's like Western Digital drives in that it needs different jumpers depending on whether there's a slave drive on the cable. Master or master with slave. Having the jumpers wrong can cause exactly the problems you're reporting. Annoying if you often add/remove slave drives. Here's their pic for normal full capacity 16head use:
<img src="http://www.hitachigst.com/hdd/support/d120gxp/16lhjum.gif">
Looks like you want the last config. I'm looking at the information <a href="http://www.hitachigst.com/hdd/support/d120gxp/d120gxpjum.htm">here.</a>
For Disk 2, the Maxtor 250, (model 4A250J0?): A "spare" position generally means a place to store an unused or spare jumper. It has the same effect as if you stored the spare in a sock drawer. Often the "sideways" positions are similar in that the rows are not connected so jumpering them is just a way to store the jumper. Depends on the drive.
According to Maxtor's sometimes flawed docs the positions are:
<img src="http://maxtor.custhelp.com/rnt/rnw/img/enduser/m_a1.gif">
It sounds like you want this to be your slave drive, so leave the jumper off or put it on the spare (4&9) position. The drive should be connected to the center (grey) cable position.
Since I don't know the age of your system I'd recommend doing things in this order to ensure things are detected as you expect:
1) Disconnect both drives. Leave the IBM drive jumpered as master and connect to the end (black) cable position. Power up the box and use the BIOS auto-detect to make sure the drive & capacity are correctly recognized. Save settings, boot. Worked? Shut down.
2) Powered off again, connect the Maxtor drive jumpered as slave to the center (grey) cable position. Power up and use the BIOS auto-detect again. If it's recognized then save & boot.
**Of course if the pics I posted or my info don't seem to match your drives then stop & double-check model numbers vs. specs.**