Feedback received from one of the forums I posted this article on was that the islands on the sub-merged plateaus in the Caribbean may simply have been warnings to sailors of shallow waters in those areas. This sent me back to the drawing board (actually, my map books and the Internet in search of topographical information about the ‘shallow water’ areas of the Caribbean). I soon discovered the 1625 map of the Caribbean by Henry Briggs (below, centre), which clearly differentiates between shallow waters (dashed lines) and islets within these regions. What happened to these islets?

I contacted several leading authorities on oceanography in search of high resolution bathymetry maps, who were quick to point out that many of these islands (typically sand banks one or two meters above sea level) had been washed away by hurricanes. A good example of this is in fact the Dry Tortugas (E on my figures)
http://en.wikipedia.org/wiki/Dry_Tortugas, of which some islands have disappeared as late as 1875.
Based on this evidence I have to conclude that the mapping of the Caribbean most likely had very little to do with maps dating from thousands of years before and that the information must indeed have been obtained by the early Portuguese and Spanish explorers.
The same cannot necessarily be said of the Brazilian islands, though,
unless the disappearance of islands B to D and the second island of group E can be attributed to some (other) kind of natural phenomenon active over the past 500 years (any ideas?). The island group E is visible from the sky (NASA shallow topography map below), but the others are definitely deeper below sea level. The Encarta Interactive World Atlas ocean floor topography seems to be in error (see Fig. 1.62a) as it suggests that these ‘islands’ are more than 90m below sea level, which does not appear to be the case judging from the other files.

Hires images of these figures can be downloaded here
http://www.riaanbooysen.com/terra-aus/87-terraproof1?start=9