Logs attached.
Today I discovered another anomaly. When I start WinUAE (it can be even just plain kick 1.3 screen with the basic configuration), minimize it on the taskbar, and then click on the icon in the systray, it becomes unresponsive and icons on menus of different Windows programs start blinking like crazy (and the system acts strangely until I kill the WinUAE process).
Log files
1 - this is taken with the VirtualBox in the background and mentioned pauses.
2 & 3 - Issue with the systray click (2 - advanced configuration, 3 - kick 1.3)
WinUAE_logs.zip