Hello everyone and thanks for your time and help!
I will present you problem-solving addicted maniacs with a rather curious case indeed.
I reinstalled Windows and Cubase the other day and now Cubase is acting up.
I am currently using a more recent driver for my sound card (M-Audio Fast Track Ultra 8r) than before. However, I tried the old one and it makes no difference.
I use Windows 7 Home 64-bit, and Cubase 5.5.3 64-bit.
I am using the same version of both Cubase and Windows as before.
I use JBridge for my 32-bit plugins.
So, I notice 2 distinct differences/problems to my previous install.
Firstly, when I open media bay or any plugin’s list of presets that stores them in the media bay, Cubase has to load for about 2 seconds and I get the spinning-round-blue-mouse-loading-win7thingy for a cursor. Also, the Cursor flickers really fast between the load icon and the regular cursor, as if Cubase is loading several small files really fast (which it is). It may not sound significant, but this never happened before.
Secondly, and more importantly, I get ASIO Time Usage spikes when holding the Alt-button. In detail:
When I hold down the Alt-button to get the Split-tool and move the mouse (while audio is playing back), ASIO Time Usage spikes and the audio stutters.
NOTE: this ONLY happens when moving the mouse, not by just holding Alt. Also, it only happens on Instrument Tracks when you hover the mouse over a point which contains a block of MIDI data. On Audio Tracks, it’s the opposite. It only happens, when there is no audio file below the mouse. It does NOT happen, when I select the Split-tool from the menu by right clicking, only when holding the Alt-button.
Additionally, performance seems all-around worse. I get the occasional click and pop in audio, on songs I used to run with a buffer of 256 sample rates with no problems. These clicks seem to happen at the same rate (maybe once or twice per 8-minute song) even if I crank the buffer up to 2048 samples. Lastly, jumping between sub menus, in Device Setup also triggers clicks. None of this EVER happened before reinstall.
First I thought that, my hard drive is getting old and wiping it and reinstalling was too much, hence the first problem. Nevertheless, I am clueless about the second problem, maybe it’s just a preference option somewhere, that I missed. 
Thank you so much for reading this and sharing my frustrations!
EDIT 25.5.2014
Second problem solved by fresh reinstall of Windows. First problem still persists, but I’m gonna blame it on my stone-aged hard drive.