Turns out my finely honed archaeo-sense didn't lie to me. Chris Cunnyngham discusses the truly bizarre reality of the context of this find and finds it rather weak (go read the piece, you won't believe it!), concluding that
So, boiled down, this is what we have: A man buys an old building, pronounces it a nation, secedes from his country, proclaims himself Prince, conducts archaeological digs and claims to have found three Templar skeletons and a nail that may have been a venerated relic of a crucifixion. And if it was a crucifixion nail it was one of thousands available.
Sounds a little sketchy.
To make matters worse, yesterday Portuguese archaeologist Élvio Sousa, soundly debunked the whole report via a scathing statement on the CEAM (a Portuguese archaeological institute) web site, of which I reproduce the English component here:
The news published yesterday in England, on the assumed Roman relics found in archaeological excavations carried out at Fort São José, erected in the eighteenth century, at Funchal Port, Madeira, requires the following statement from the Scientific Council of CEAM:
1. Considering the scientific archaeological work done by CEAM at Fort São José (2004-2006), it is manifestly false, the news of the discovery of Roman objects, especially in an area (dig) that corresponds with the excavated area.
2. This dig identified, to the bedrock, objects dating from the eighteenth, nineteenth and twentieth centuries, although there are some traces that can date back to the seventeenth century.
3. The news of the findings of Romans relics is a “fantasy,” even more ridiculous by the sensationalist news of a wooden box (incredibly preserved, near the sea, over two thousand years), with three skeletons and three swords.
4. The nail that illustrates the news, if discovered inside the fort, is just an object used in residential constructions during the early Moderns times (seventeenth and eighteenth centuries). Many nails like this were found in the excavations (2004-2006). Equally, the references to skeletons are also a creation, to give emphasis to the mythical theory.
5. This view is supported by the British archaeologist and expert in Roman archeology Brian Philp (Kent Archaeological Rescue Unit) who has been following the present study of archaeological materials in partnership with the Scientific Council of CEAM.
6. In conclusion: this is pure imagination, without accuracy and scientific credibility. We are not familiarized with Mr Christopher Macklin and Bryn Walters and we do not recognize in them, any authority in the findings within this Military construction.