Just a thought... Look into what allocation system you are using... if either partition is over, I think it is c. 35Gb or so, you must use NTFS on it. With a drive the size you indicate [110Gb], I would think, to run 98SE or any of its tools; for example, you would need to downsize one or the other partitions to below that figure...and maybe set up three partitions of one size or another.
There is an excellent "discussion of this topic at File Allocation Table - Wikipedia, the free encyclopedia
But, what do I know, I'm old and grey
I know, that when I got [had built] my latest computer, I wanted something big and bad, but I got caught in the size is not necessarily better
myth. Not knowing any better, I immediately found that I could not run my beloved 98SE, and so had to opt for XP Home...and the NTFS. I have since learned to adapt, as if I had been zapped by a BORG
unit...resistance was futile
...but I still miss the control I had under a FAT32 system. I would, in all likelihood, opt for multiple drives of a smaller size
then a single large drive, in future...and get back to FAT32 and 98SE...and thus back to a full DOS environment. This new fangled stuff is only to enhance MS profits and overcome the issue time wasted helping us overcome MS-OS's flaws...not to give us any degree of pleasure in the process...bummer ;(