Because the TV movie depicted the regeneration of the Seventh Doctor into the Eighth, thereby creating a direct link to the original series.
One possible answer is that Russell T. Davies only recognises television episodes as "canon". In the Forward to the Big Finish Guide, Davies even states as much. The TV Movie aired on television while Shalka was a webcast.
The DVD release of Shalka pretty much spells it out: the BBC only counts live action as canon, and BBC Wales proceeded with planning the revival apparently unaware of the webcast. And the writer and producer of the webcast state clearly that had they known a TV revival was planned, the webcast would have been cancelled outright.
The expanded universe of the novels has suggested that Shalka takes place in an alternate universe alongside the other Ninth Doctor depicted in Curse of Fatal Death.
It should be noted, however, that at no point in Scream of the Shalka is the Doctor ever actually referred to as the Ninth Doctor. Therefore he could well be an unspecified future incarnation alongside the Tom Baker "Curator" and the Valeyard. (Much as no incarnation number has been or likely will be assigned to Lady Trey, the future incarnation of Romana introduced recently to the audio dramas.)