The problem isn't *when* the autograph was taken or on what item the autograph was written on. The problem is ascertaining whether an autograph is genuine or not. There are many Freddie autographs out there for sale, and some of them have certificates of authenticity but often there is simply no way to tell.
All of the band's autographs are quite easy to fake for an experienced forger, and so it can be almost impossible to know if you're buying an original or a fake, even if there is a certificate of authenticity. There are some proven examples out there and it seems that the items which achieve the highest prices are the albums signed by all four members of the band - if they can be proved beyond doubt. It's likely that even Brian May wouldn't recognise whether a signature was his or a forgery at times.
The other thing is, even the Jacky and Val at the fan club were known to do some autographing on the band's behalf..... There are posts about that on this site. I believe it's now thought that a sizeable number of items sent in to the fan club were actually autographed by the fan club staff, and that it's quite unlikely that any member of the band just decided to drop in on the fan club unless they had a reason.
On a side note, the Queen Official International Fanclub is not actually owned by a Queen company. It is owned by "Gunsmith" productions - thats the maiden name of Jacky and Val Gunn, and Jacky's husband Peter Smith. They are basically licensed to do the magazines, organise the convention, and sell Queen Fan Club merchandise etc, since 1993. Before that I don't know if the fan club was owned by Queen themselves or not.
No, Freddie's autograph isn't more valuable according to the year it was written. It's value is in whether or not it can be proved genuine.
For example, a genuine signature on the Innuendo LP - and there's a few of those around - isn't worth more than a genuine signature on the "A Kind of Magic" LP or even the "News of the World" LP.
However, with things like this, it's always speculative. If you were shopping for an autographed item, would you rather buy a signed copy of Innuendo, Barcelona, or The Miracle? Or would you rather buy a signed copy of "Hot Space" or "A Kind of Magic"? Or would the title of the LP not bother you as much as having the genuine autograph?