Actually, I'm not sure when the CF begin their level 3 background checks, perhaps somebody else could clarify this?)
Indeed, CSIS does the background check for the CF. However, DPM Secur2 does the primary verifications and the PRIORITIZATION. I am in the process of getting a level II sec clear and it's been more than 6 months as we're speaking.
I personally know about 30 people in the Signals Officer trade. Many positions in these trades are not "hardcore" level III. There is no rule bending for hardcore level III, if you need it for operational purposes, it will be fastracked and you'll not be able to be posted at this position until you get it. I have seen site access clearance (that's level III+) granted in less than 3 weeks. It rarely occurs, but my point is that if you absolutely need it, you'll be processed faster.
The policy is that they can still employ you even though you do not possess the standard trade security clearance. Unless you're afraid of being "denied" a security clearance, it is not likely to affect your enrollment process.
However, some classifications requires that you get a security clearance BEFORE you enroll. Public domain example of these are OPM (officer of the military police) and the military police officers themselves.
IN order to get a better idea of the time CSIS takes to process security clearances, have a look to their latest public report:
http://www.csis.gc.ca/eng/publicrp/pub2003_e.html#4f
The average processing time for level III access is 72 days. This information has to be interpreted in context. It only accounts for the time between the issuance of a request to CSIS and the time the investigation report is returned to DPM Secur 2. DPM Secur 2 has to act upon CSIS recommandations, this adds further delays.
As well, the average processing time is only good when you can get the standard deviation on all the requests. It is possible to get an average of 72 days by having half of the request taking a very short amount of time and the other half taking a very long amount of time. So that 72 days means squat.
Hope this helps,