I am actually a FIOS tech support rep. I can tell you this is a thorn in our side. In all honesty, this is a problem I see at least once a day.
Is there a problem with the FIOS set top box? Yes. Is there a problem with the Samsung HDMI port, yes. Let me explain.
I have gotten fed up trying to explain to customers their brand new Samsung Tv continues to get the "searching for signal" error. I called Samsung for the answer. I was told by the SAMSUNG rep they have a "second generation" HDMI port on their TVs and are not always backward compatible. I asked him what this "second generation" HDMI port was, and how it differed, but did not get any answer.
The SAMSUNG rep informed me that MOST of the TVs have a firmware upgrade available on their website, which I confirmed.
Regardless, the issue is being addressed on both ends. Samsung has offered the firmware upgrade, and Verizon has created a new 1.7 firmware for their set top boxes. The typical workaround is to use component cables at the moment. A common mistake people assume is they lose resolution by using component. This is not true at the 1080i resolution. Component will support up to 1080p which FIOS is not capable of at the moment. There is no loss.
Believe me, it sucks telling people this, especially because I know Samsung makes a great product. Everyone is aware of it, and we are taking measures. I have a Samsung DLP LED tv which seems to be immune to this issue, but there are also a load of Samsung Tvs that arent. In my experience, this ONLY affects Samsung LCD and Plasma Tvs. I have not yet had any issues with the DLP or DLP LED tvs.
I apologize for the lack of knowledge of the rep that you spoke with. There are some out there, but for the most part we are all very well educated (at least in my office). Verizon puts us through at least 8 weeks training before we even touch a phone, and training and education is ongoing.
Verizon FIOS hasbeen a great company to work for, with AMAZING pay and benefits, especially considering what we do on a daily basis.