PER is issued only after STEP 3 (ELIGIBILITY REVIEW) in the FSW2174's post below. But CAP is updated on CIC Website after STAGE 1 (Completeness Check by CIC, Sydney). So as per cic website, the page has been modified on 3rd Sep 2013.
SO as on 3rd Sep 2013, 1399 Application received have passed the STAGE 1 "Completeness Check by CIC, Sydney".
Hence out of these 1399, some may have been charged and PER issued, some may have been only charged, some may neither have been charged nor PER issued, but certainly all these 1399, have passed the STAGE 1 "Completeness Check by CIC, Sydney".
Also on CAP Update page, CIC has a put a note:
"Note: Due to the large number of applications we get, we cannot check that each one is complete on the same day it gets to the office."