The original reprints of the DW books were published by Flaming Cobra, a subsidiary of Mongoose Publishing. However, they were just the publishers - the DW licence was owned by Magnum Opus Press at the time, so if you see Magnum Opus/Mongoose Publishing/Flaming Cobra, these are effectively the same edition (although there are multiple printings of some of the books, which may or may not include errata and/or be of greater or lesser quality than the initial print run - as a die-hard fan, I tended to purchase editions as soon as they came out, so can only comment on first printings).
I haven't actually bought a physical DW supplement since Magnum Opus lost the licence, so can't compare print quality between the two licence-holders' editions, but I can tell you that, in the UK at least, the Magnum Opus edition of Sleeping Gods suffered from some quality issues (to the point that some of the maps were illegible - if I hadn't had the original series of books, I would never have been able to produce these:
http://cobwebbedforest.co.uk/library/ma ... s=sleeping, which you might find useful if you end up with one of these editions).