Hello Anton,
the root cause of the cut off toolbar areas is not SAP GUI, and therefore can not be fixed in a SAP GUI patch. In SAP GUI for Java it only looks better because you are running it with the default font size.
If you set it to e.g. 16 or 18, you will see similar results also with SAP GUI for Java.
Unfortunately, the application sets to toolbar heights to absolute numbers independent of the font sizes used. Therefore increasing the font size results in what you show in the screenshots.
The solution would be to set the toolbar heights with relative sizes to be able to display toolbar buttons with bigger height. This needs to be corrected on the application side. I only can recommend to open a support message describing the issue on the component of the affected ABAP application(s).
The issue related to the checkboxes is also happening using SAP GUI for Java? Feel free to report this on component BC-FES-GUI / BC-FES-JAV.
I would be interested in getting more information about SAP GUI for Java hanging sometimes.
Could you please enter a trace file name in the trace dialog, so any error messages get logged and send them in a message on BC-FES-JAV?
(On Yosemite, please use SAP GUI for Java 7.30 rev 10 running on Java 7.)
Best regards
Rolf-Martin