Sorry for digging out this one - just felt I needed to contribute something
Did this a few days ago, on the return portion of a OSL-CDG-TLV (AF) TLV-FCO-JNB...stayed 2 days on the inbound, 4 hour transfer on the outbound with checked luggage from JNB.
Got quite a few questions about why I was doing this specifically and why I traveled so much (specifically short transit visits to Turkey and Morocco - MR stuff). They checked my carry on bags. One of the things in it then had an itemiser alert (don't know which and what sort of alert, and no, I didn't do anything with firearms or explosives or narcotics when in South Africa, but my backpack was with me all the time, so some sort of random contamination can't be ruled out I guess) which is where things started to get tough. Was then questioned by two supervisors in a row, rather intimidating, the last one being almost actively hostile. Remained calm, but was essentially told that I didn't have the right to know what was going on. Got a very thorough (as in "lower your pants") patdown by two people, then they started to cram all of my belongings out of the backpack into my checked bag. This included one of two cellphones, my work laptop and a battery pack as well as my home keys, cigarettes and lighters.
I was then told by one of the agents that I would only be allowed to take one cell and my money/passport and the necessary credit cards, all the rest needed to be checked. They shipped my backpack separately in a carton, possibly together with my headphones. The backpack didn't arrive at my final destination yet and said headphones are nowhere to be found in my luggage.
I was told this was a decision by security. I did not raise the question how lighters and batteries in hold luggage are possibly more secure. I do suspect that if the trace alert was for explosives and they couldn't find anything, then it might be a good idea to separate the passenger from any possible explosive device physically...but don't know if that's what triggered this.
Took me two-ish hours in total. I get the rudeness of the agents is part of their training, and apart from those asking questions, the other people involved were reasonably friendly. I don't recommend transiting via TLV though.
Hold thumbs for the backpack and the headphones actually arriving at some point...the backpack wasn't expensive, but the headphones kinda are.

The morale of the story? Don't mileage run via TLV, especially not if you frequently transit via Turkey