FI light comes on with Quickshifter

[NightHeat]

Got an 04 GSXR 750.  Using a Cordona GP quickshifter and whenever I shift, the FI light comes on.  I understand that the fuel being cut by the shifter would cause the computer in the bike to think that there is a problem,  but should'nt the Power Commander be telling the bike's  ECU that everythings Okay?     Any ideas or is that just a normal operation in using a quickshifter?