I'm guessing by the description given, that the CF card is not seen.
If it's formatted in the camera, the PC will see it by default. Formatting isn't the issue.
I'm guessing that it's a connection problem, or is the CF card reader device some thirdparty 5 1/4 " bay drive type 'onboard' type.
Is the connection to it secured properly?
Is the CF card reader the same physical device .. ie. if a 3.5" or 5.25" multicard reader device are they the same .. or is the SD card reader a different physical unit.
If this onboard CF reader is one of the slots in a multi port device, where only the CF reader is the only one not working, try a new driver from the manufacturer.
FWIW tho, even this may not help.
I have a Cool Panel III multi port 'onboard' card reader. It has all manner of connections and PC sensor readouts too.
Pretty impressive looking.
It reads almost all of my cards bar one. I have Sandisks and Lexars and PQI branded and others I can't remember.
But I have this one super fast Patriot branded CF card that this on board CF slot just won't read at all .. ever, no matter how many drivers I try to load for it.
It just happens to be one of those incompatibilities that I've learned to ignore.
It then forced me to get a Lexar USB3 card reader tho .. which was a blessing. This device reads all cards without trouble .. even the Patriot card that the other one won't.
So for the sake of completeness .. is this a new system? Is the card reader a new device?
If you plug in the CF card, and go to device manager, do you see any devices in the list with a [!] (exclamation mark)?
If so, check for drivers.
Under the heading Disk Drives, you will see all of the external card type devices listed there.
As an example my system has this 5.25" bay device with multiple slots, and they are listed as:
Generic Compact Flash USB Device
Generic SD/MMC USB Device
Generic MS/MSDuo Pro USB Device
.. and more.
These (and more) are the slots only on the 5.25" bay Cool Panel device(which for all intents and purposes are 'onboard').
All the media slots are connected via the one internal USB cable.
The other listing I have for media slots is the USB3 Lexar reader which shows as follows:
Lexar CF USB_3_0 Read Device
Lexar SD USB_3_0 Read Device
I know that if one of those groups goes down, then it's a connection issue, or the device is dead or something like that.
It's unlikely that one of the listed devices in the group will drop off the list by itself.
They're interconnected.
If you see a list where one of the listings in a group is not there, then it's probably an internal malfunction in the device.
(alternatively a driver problem, but less likely)
The driver for my Cool Panel bay is a single file, which basically converts each drive slot into a readable device via a USB connection.
They're either all there or not.
Which USB port are you using for conenction .. to the camera, to the external USB reader .. etc.
Each port may connect to a different USB port internally.
If the camera is recognised and the CF card with it via that method, did you connect the external reader to that same USB port as you did with the camera.
(if so this is beyond strange, it's Twilight Zone territory!
)
Again, connect up as much of this stuff as you can and check device manager for any anomalies.
(you may have to click on each sub heading to see all the devices .. eg. maybe for the USB gear list) .. and all drives in the Drives list .. etc.