So, I think clarification is necessary.
First- What the Directors on up are pretty much solely focusing on now (you'd think they would have more important stuff to do, but apparently not)--- is the Average Hours report. The other data points (badge swipes, COU, etc) are still there in the background and a part of the Presence Reporting. But it is the Average Hours report that is getting all of the scrutiny. And to the OP's point, EVERYONE knows it has issues.
So, in the current climate it is incumbent upon YOU to make sure it is reporting correctly. No one else is reviewing the validity of it on your behalf. If it is all wrong, and you are being shortchanged---if you do nothing except complain here, it is going to come back to bite you. You need to open a ticket for every single day that is incorrect. You need to keep a very close eye on it, and track your own time very closely. Your only recourse when HR comes calling will be acknowledgement that your hours are underreported and your ticket numbers showing that you are aware and are trying to get it addressed. If you have done nothing, they will assume the hours on the report are accurate and you're toast. This is all really sad and pathetic when you take a step back and look at where we are. It is unfathomable to anyone that works for a normal company, but here we are. If you want to stay, you have to play this game.
Second, while from an employment law perspective you are certainly "on the clock" once that badge is swiped to let you in the door and you are on premise...for the execs here using the flawed Average Hours reporting, make no mistake that your day does not start until you PC is first pinged when connected to the LAN. Depending on how far they want to push this , if they were to start firing people that are 15 minutes "short"---they are certainly going to be inviting a lot of litigious action.