I use hipchat 126.96.36.1992 installed on Ubuntu 16.04 Desktop
whenever I receive a message, it appears on a white box which has no border and the text is seethrough. this makes it rather difficult to see when it appears on top of something light coloured, see attached
This looks like an issue with graphic card driver. So I would suggest you update your graphic card driver to the latest release and use the official driver.
Additionally, if you still have the same issue after updating your graphic card driver, please use the following parameter to start HipChat which disable the client from using GPU:
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