As I noted with the Oilers, there are several acquisitions who hadn't played in a single game against the Flames in the two years prior to coming to Calgary. These players were David Hale, Mike LeClerc, Cale Hulse, Peter Vandermeer, Kyle Greentree and Lawrence Nycholat. In other words, filler. Still, in addition to these six, another twelve players had three or fewer games against the Flames leading up to their acquisition and these twelve had a much bigger role on the Flames. This means that 18 out of 33 players did not have a significant track record against the Flames before being acquired. This number is consistent with that put up by Kevin Lowe and (to a much smaller degree) Steve Tambellini in Edmonton. I think this is good evidence that this isn't a main factor in the player evaluation of most players.
The rest of the results look more random in this case than they did for the Oilers. In terms of point totals three players did significantly better against the Flames, eleven players were about the same and one player was significantly worse. In the case of the Flames how players performed against them looks like it may not have played much of a factor at all. In the case of some players it seems like other factors probably played a bigger role. Some players had played for the Flames before (Conroy, Hulse, Leopold and Lundmark), while others were familiar to Darryl Sutter from his time in San Jose (Friesen, Smith, Stuart, Zyuzin). In other instances the player may have been a favourite of Mike Keenan (Bertuzzi, Jokinen) or had played a significant role on the Tampa Bay team that beat the Flames in the 2004 Stanley Cup Final (Sarich).
Still, there are cases like Curtis Glencross (and the Flames sure payed for taking a chance on him! Wait...) where his performance against the Flames looks to be significant. Perhaps it was also something that drew Sutter to players like Bertuzzi and McCarty who, for whatever reason, were statistically more successful against the Flames than the rest of the league. Furthermore, neither team signed many players who vastly underperformed against their new team (congratulations to Wayne Primeau!), although just looking at point totals might be misleading here. I can't imagine the Flames were wowed by Roman Hamrlik's -4 over two games. My conclusions after looking at the Flames haven't really changed. Recent performance against the new team is most likely a subconscious factor in signings and trades. The effect looks to be small in general but probably plays a big role in some isolated cases.