I have similar (or the same) issue - from time to time a quick popup appears and instantaneously disappears, making it impossible to spot. I immediately opened console and watched what happened:
10.2.2013 12:18:59,352 UserNotificationCenter[5163] *** WARNING: Method userSpaceScaleFactor in class NSWindow is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead.
10.2.2013 12:18:59,604 _softwareupdate[5169] audit warning: soft /var/audit
10.2.2013 12:18:59,604 _softwareupdate[5170] audit warning: allsoft
10.2.2013 12:18:59,605 _softwareupdate[5171] audit warning: closefile /var/audit/20130210111445.20130210111859
10.2.2013 12:19:08,510 System Preferences[5179] Cannot call setInetDServiceEnabled:enabled without first being authenticated
10.2.2013 12:19:03,425 ntpd[5188] proto: precision = 1.000 usec
then, immediately these lines began populating:
10.2.2013 12:19:04,200 SubmitDiagInfo[5157] Submitted crash report: file://localhost/Users/(me)/Library/Logs/DiagnosticReports/cocoAspell_2013-02-0 4-223143_mac.crash
10.2.2013 12:19:05,120 SubmitDiagInfo[5157] Submitted crash report: file://localhost/Users/(me)/Library/Logs/DiagnosticReports/cocoAspell_2013-02-0 6-211421_mac.crash
10.2.2013 12:19:05,937 SubmitDiagInfo[5157] Submitted crash report: file://localhost/Users/(me)/Library/Logs/DiagnosticReports/cocoAspell_2013-02-0 6-215341_mac.crash
10.2.2013 12:19:06,694 SubmitDiagInfo[5157] Submitted crash report: file://localhost/Users/(me)/Library/Logs/DiagnosticReports/cocoAspell_2013-02-0 7-205919_mac.crash
10.2.2013 12:19:07,475 SubmitDiagInfo[5157] Submitted crash report: file://localhost/Users/(me)/Library/Logs/DiagnosticReports/cocoAspell_2013-02-0 8-193007_mac.crash
10.2.2013 12:19:10,233 SubmitDiagInfo[5157] SubmitDiagInfo successfully uploaded 691 diagnostic messages.
Have you ever (also in your previous macs, if you restored stuff from a timemachine backup after getting MBP retina) installed Aspell? I mean, if you installed a language that's not supported by spellcheck by default (in system preferences - search for spelling). If there's a language with Aspell listed, try to disable it. I also deleted ~/Library/Services/cocoAspell.service.
I tried and will be checking if the issue reoccurrs.