Thanks For the response. On the hints your assertion that I must treat them as two different programs is surely patently false (perhaps you misunderstood my problem, or it wasn't explained properly). My tree is stored at ancestry.co.uk - and i use Family Tree Maker's TreeSync to keep the two in sync. Changes are reflected in both, obviously. The same should be true of hints too - its ancestry.com that is generating them after all, not the program! If you clear a hint on ancestry.com - why should you expect to have to clear it again in a tree that is synced to ancestry.com!
No, I rather think this is poorly implemented feature, or a bug. Digging deeper, reveals that the type of 'hints' that are not 'synced' across are the member tree matches. Other types of hints (records etc) are synced. This is disappointing, because you certainly do not want to be doing the work twice across both website and program.
As for my disappointment with the software - well I shouldn't have muddied my main question with a digression, but since you kindly commented - i was comparing purely to the ancestry.com website itself. One of the advantages of desktop software, surely, should be a greater richness of UI than afforded by the website. Instead, i find that steps that are well handled by the webiste (eg merging of hints) are handled poorly in the software taking many more steps. The navigation is also poorer, and the close integration with the actual website, means that the sluggishness I now see in ancestry.com (which has got progressively worse over the last year) is completely reflected in the software - hence my comment about zip,