Something to consider ... There are (2) 4 pin connectors on the bike. They are the same style except only (1) is the data link. The other is an accessory power plug.
On some models these plugs are somewhat close to each other. For example, the Acc Power might be under the seat and the Data Link under a side cover only 8 or 10 inches away. On some, the Data link under one side cover and the Acc Power under the other side cover. It is important to make sure you are using the correct plug. Obviously the Acc Power plug will not work.
How to tell them apart? The Data Link will only have 3 wires going to it. Probably Gray, Black and Lt Green/Violet stripe. The Acc Power will have 4 wires going to it. Probably Orange/Red, Black and Red/Yellow.
I have seen this mistake made more than a few times. The other common problems as mentioned above, Run Switch off, Key switch off.
The VIN number issue is typically related to '01-'03 Delphi fuel injected bikes that had a malformed VIN installed directly from the factory. This issue can be fixed with the digital tech at the dealer. The biggest problem is getting them to realize they can fix it. It requires loading the Stock Factory settings and entering the bikes correct VIN.
An all together different issue is if the ECM needs to be replaced. I don't have an exact answer but there are 2 schools of thought regarding the SERT with a replaced ECM.
1 - The replacement ECM can have the bike VIN installed and the SERT will work with that ECM since the SERT key "marries" itself to the VIN.
2 - The SERT key doesn't actually "Marry" itself to the VIN but rather a Serial number of the ECM. The SERT software then returns the VIN from the ECM. If a New ECM is installed, it has a different Serial number even though the correct VIN was installed the SERT will not work.
I have not had the chance to personally test either of these theories so I can not say which one is correct. I have heard (here-say) others make claim to both and I do not believe both can be correct.