They wouldn't need to know you had another passport, only that you were not entering the same way you did last time. Thinking about this a bit more, the main data points you enter for the ETA are (from memory):

(a) Name, first and last
(b) Date and place of birth
(c) Passport number
(d) Country which issued your passport

Presumably the DIMA computers scan all of those fields for matches or inconsistencies, or other stored information (like known bad guys). For instance, if you had previously been deported from Australia or overstayed a prior visa, you would expect the computers to ding you when you applied for an ETA, and the only way they could do that is by matching stored information with the information being supplied for purposes of obtaining the ETA. In davistev's case, I wonder if when the computers ran that information they found that davistev had previously entered Australia (several times, no doubt) but that this time the first two points didn't match the passport number and/or nationality on record. In that case I would not be the least bit surprised if the computers were set to reject the ETA and require an in-person interview to explain the incinsistency. No need for DIMA to link to information about carrier/cash purchase on day-of-flight etc, just a simple mis-match of stored records. The commonwealth government has some of the best data-matching computing around, as anyone who has (or hasn't) filed a tax return and has a HECS bill well knows.