I understand that the actual charge against Mr Paladini is " using or seeking to pay an unauthorised agent" so I think the FA are pretty certain in their grounds for this charge.
Also the FA apparently instructed QPR by the FA to take the steps required to make this transfer legitimate in September last year, and it was the documents submitted to say it had been done which have attracted the false documents charge.
QPR did however buyout the 3rd party involved in January 2011 so it does leave you thinking what was the registration status from September 2010 - January 2011.
Even if the FA accept that the 3rd party involvement prior to September was a geniune mistake then QPR would likely only get a fine, but submitted false documents and being found out boy are they in the brown smelly stuff.