No. The order of installation doesn't seem to matter (in my situation). I have been successfully using the Gemulator Explorer for a very long time and have been able to make perfect images to CF's and take perfect images off of CF's (for archival purposes only).
(I'm assuming you're wanting to write an IMAGE TO CF)
1) Be at your Win98 desktop.
2) Plug in your sandisk reader. The USB driver will pick up on the installed hardware and put an icon in your taskbar (where the clock is). Ok. Now your computer recognizes it as a drive. Keep in mind that the native file system of windows is totally different from the filesystem of QNX (once you've got that, everything else is a piece of cake, for example if you have a CF with a QNX image on it, it seems to me that in several posts, people expect windows to be able to read a QNX file system. Nope, not going to happen... i'll explain this later).
3) Ok. Insert a CF card into the cf card reader/writer.
4) Verify the light on the front of the drive is lit.
5) Know where the image is in you're computer's file system that you want to put on the CF (example: C:\images\uberBOOT.img) This is the name of my really good basic back up with the Shell hacks, etc.
6) Open Gemulator.
7) Your CF drive will be assigned a drive letter. For example, mine is 'G'. If you need to know which one is your CF, then open up My Computer and the icon for the drive will be the same as the icon of the CF drive program in the taskbar.
8) In Gemulator, DO NOT click on the drive (G) labeled "MSDOS files on G:\", you need to click on the drive that says, "SCSI ctl:2 dev:0 (SanDisk ImageMate II)" (the word sandisk should give away the right drive to use) and the light on the drive should flicker.
9) Then click in the menu for "Write Image file to Physical Disk". Select your image "C:\images\uberBOOT.img". And, the drive should begin writing activity.
10) When the drive is stopped. Remember, the file system is now QNX... NOT MS-DOS (FAT16 or FAT32... FAT stands for File Allocation Table)! You won't be able to use windows to read a single file off of the CF disk!!!!! You will only be able to use Gemulator to strip an image of the entire CF disk onto your harddrive (and windows will see this as one big file, but it's really a filesystem inside of a file in a different filesystem, like a green folder inside of a blue folder, or something).
Now, I hope everyone understands why Windows can't read the QNX files off of a CF image of an Audrey. Because, they use different file systems.
Good luck to ya,