Are you powering it with a fresh 9V battery using the supplied connector? Is the connector and USB cable pushed in all the way? That's all I can think of.
Reset a PCIIIUSB
To reset the Power Commander, connect it to the software and power it up using the 9-volt adapter. Once you have communication established go to the "Tools" menu and select "Environmental Options". Once you have selected that option a window will appear that has a black rectangular button at the bottom that reads "Reset Power Commander". If the button is not visible then you would have to hit the "Control" and "R" keys at the same time on the computer keyboard to display it. If you are using a custom map or one that has been altered, make sure you save a copy of your map first, as the reset procedure will zero out the map and reset the power commander to the factory default settings.
PCIII USB firmware update failure
If the Power Commander III USB will not complete a firmware update using the control center software, check the following. Make sure you are using the latest control center software.
Make sure you are using the correct version of firmware for your device.
Make sure you are using the 9-volt adapter, and the battery is producing more than 8.5 volts.
Check the current version of firmware, it needs to be 1.0.0.20 or newer to update using the control center software.
If the firmware update still fails, the firmware programmer module will be needed to update the firmware.
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It sounds like you might have to send the unit back to get it re-flashed by the factory.
Would it be worthwhile to get a Power commander for my 00 Fiy 5th gen? she doesn't have the 02 sensors since the header have been replaced.
If you're looking for more horsepower, no. If you're happy with the throttle smoothness on your stock bike, no. If you're looking for a bit more throttle on/off smoothness, then maybe yes.
My '98 5th gen came from its previous owner with powercommander, de-snorkled, de-pair-valved and is super smooth compared to my '07 6th gen which often exhibited lean throttle jerkyness and occasional stumbling at certain temperature/humidity combinations.
I can't say if it was the powercommander that made the difference or just tighter emissions requirements for the '07. But I won't be removing the PC, because the bike runs great as is.
My bike is totally original from what I can tell,if I could get her to run right I think I'd be happy as she is,I think I may have a reg/rectifier problem or stator because she cuts out at idle sometimes and can be reluctant to start,new battery just fitted before I bought her.
I must look into this snorkel/pair valve mod, this bike has the original end can,which I think I prefer to the high level micron pipe on my last 5th gen,I can hear the GDC better,don't know why I ever contemplated getting the 6th gen,they are also a great bike but these 5th gens are a super bike in my opinion.
with the oem end can I have the option to fit side panniers now if I decide to do some touring with her.roll on springtime.
Would it be worthwhile to get a Power commander for my 00 Fiy 5th gen? she doesn't have the 02 sensors since the header have been replaced.
it does give a way smoother delivery - dont see any change in HP but definitely runs better. With Aftermarket pipes and K&N filter - the ride is much much smoother.
I just realised that the exhaust does have the 02 sensors,the headers look brand new,I can't tell if they are the original system,if it is this bike must have been kept like a baby,it still has the oem end can too,
I might look into getting an end can and a kn filter later on,also read up on removing the snorkel/pair valves and then get the power commander,I intend keeping this bike as long as I'm able to keep riding bikes.I suppose it's nice having her all original too though,definitely a future classic.