Credit to Kris De Volder and 'Alex' for the following explanation and work around, as commented on the issue I opened at this address https://issuetracker.springsource.com/browse/STS-3922 and mostly just directly quoted here to provide a complete answer for this question:
"The problem is coming from the following system properties [... as they contain] values that are not serializible. The properties are:
osgi.configuration.area.default
osgi.user.area.default
osgi.user.area
"As a workaround people can add -D properties to their STS.ini, eclipse.ini or GGTS.ini to set these properties to the values they used to have in Eclipse 4.4.1
-Dosgi.configuration.area.default=null
-Dosgi.user.area.default=null
-Dosgi.user.area=@user.dir
"We are also adding this workaround to Gradle tooling in upcoming 3.6.2 release so that when the gradle plugins are installed these props will be added to the .ini file automatically.
"Also worth mentioning that Gradle seems to have patched this problem on their end as well so another workaround is using Gradle 2.2.BUILD-SNAPSHOT. Set it via Gradle Preference page in the tooling or by setting in the gradle.wrapper in your gradle project(s)."
So there you have it! A simple fix which you can either apply manually yourself, or through an update. And I can confirm that it works.
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