If trying and install Linux with many partitions (/, /usr, /usr/local, /home, /tmp, ......) which obliges Linux to create an extended partition, this partition is detected by Windows 98 as a new logical disk (which produces a pretty good looking offset in the drives letters). This is not like that with Windows NT. The solution i took was to create only 3 large partitions : /, /usr and SWAP, but that's not fair with UNIX administration.
This is not a bug, but rather the way that Win98 is treating linux partitions. You said yourself that NT does not have this problem.