- Is MSRT at the latest and current version (March 2016 - build 5.34.12400.0)?
- Have the tool ran and reported these 'preliminary' detections just once (when you updated the tool last week)? Or do detections persist if you run additional scans (either quick or full)?
FWIW, we have seen similar reports over the years but never a clear explanation as to why this occurs. See this probably related thread - to include sources for the following:
If the mrt.log file shows clean (no infection found) then it's likely MSRT suspected a possible threat during the scan, displayed it as such (preliminary detection) but determined it was not an actual threat before completion. The initial detection could be due to heuristic analysis or an incorrect virus signature in the database. Microsoft Antimalware software uses heuristic analysis which will automatically submit suspected threats to the server where the file(s) is checked against signature updates in the master database. If a match is found and verified as malicious, updated signatures will be downloaded in order to take action on the detection. If the detection is determinded to be a false positive, no action is necessary.
Please also keep in mind that MSRT only scans for and removes a limited number of specific malware families (a small subset of active malicious software) so it is not comprehensive... and, in general, shall not remove as many threats that might be compounded by categories such as adware, toolbars or Potentially Unwanted Programs (PUPs).
However, since you are talking about an 'abnormal number of threats being detected', and your resident AV (+ MBAM) is giving you a 'clean bill of health', I would suggest you run some additional scans (including a full scan using same MSRT and/or the MSS - if you haven't yet done so) - using AdwCleaner and the ESET Online Scanner - for a second (third) opinion.
Please report back if any detections by these tools.