Same error message "Creating a new Signiant Transfer Engine because the previous transfer had to be canceled. This session is at risk of running out of available system resources."
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I had this message after a chaotic upload of a 120 Mb app to the AppStore, using Application loader v2.7 (273), and MacOSX 10.7.3. Searching for my SKU in "Window->Lookup Status..." menu item dialog box, I noticed that there had been several Failures ("Upload Failed"), including at least one time, I decided to push the "Cancel" button in order to reboot my machine, so much this upload was slow.
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I have noticed that the Application Loader JAVA engine may still be running in the background when you quit the Application Loader application, and that it is no more visible in the "Force to quit..." list. I use a packet surveyor called "Little Snitch" that showed this JAVA engine running while only Finder was opened.
So to summarize: this message may be shown when you have cancelled one of your uploads, and just restarted a new one while the previous one (performed by a background task) was still running in background. This generates a "Warning" message, but not an error, thus, instead of the green "OK", you have a notification of the warnings, just like in XCode.
http://stackoverflow.com/questions/10548196/application-loader-new-weird-warning-about-signiant-transfer-engine