Slow upload speeds on a leased line (fibre 100Mb)

Our line was very slow recently, and our IT team suggested after running some speed tests that the upload speeds were very low (6 Mb on average as opposed to the 100Mb provisioned initially on the line).
The ISP and our IT support both sent an engineer on site to run rigorous speed tests, then our ISP decided to get BT who are the carrier involved, thinking there was a fault with the line.
BT sent an engineer on site who established there was nothing wrong with the fibre link.
However, our ISP fixed the fault afterwards by supposedly introducing a router, and now they are saying it is our equipment (firewall) that was causing the speed issues.
Isn’t it weird that after them running the speed tests on site by plugging in directly to the BT box, and arranging for BT to come out and test the line, after all this could our equipment still be in fault…please bear in mind the speed tests were tested without our firewall (as mentioned above direct connection to the BT box)
We tested the line speed , using Full duplex 100, half duplex 100 and auto on our firewall/router.
In your opinion what could cause this low speed issue on a fibre link.

Well it's highly unlikely to be actual fibre itself.

However, our ISP fixed the fault afterwards by supposedly introducing a router,

So where does the replaced router fit in the scheme of things? Sounds to me like the ISP is at fault, but are trying to recoup some of the repair costs from you guys.

Thank you for your input Zarjaz,
The ISP so far hasn't produced an incident report and in fact ignored 7 e-mails I sent over the last few days.
in your opinion, am I right to say since the tests were performed without the firewall and they were showing the same results, then the fault should be 100% at the ISP’s or BT’s kit?
Also, if it’s not bandwidth throttling or duplex settings, what could it be?
bearing in mind the ISP use a cisco router at the core level.