Strobe follow, is essentially hitting your a /follow Master command, every few seconds.

You could add something similar to your mapped keys.
Create a new mapped key, something like: FTL Target Me + /Follow.
Then have each of your regular mapped keys also run this keymap.
Not sure if that is an elegant solution, more along a brute force method.

When I run a tank toon, or a melee dps, and have strobe enabled.
And then switch to a different toon, quite frequently in melee the toons start to follow the first toon I had enabled strobe with.
It doesn't happen all the time, and is not a bug I can reproduce at will.
Another poster suggested reducing the frequency in seconds of the strobe, to at least 3 seconds or less frequently.
This is not a 100% fix for me, but I'm not running many melee toons, so its not a huge issue either.

Strobe or repeated follows, is the desired action, when you are moving from A to B and wish to re-establish follow.
It is very useful with melee toons, who will break follow from melee.
But who will then reacquire their follow target shortly after combat.

IWT is more important then strobe, at least while the combat is taking place.
You would prefer your melee to be on the target, rather then close to the team master (who might not be close to the target).
But having strobe initiate a follow, which was broken by combat, is a very nice feature.

Ideally, you'd want both IWT and Strobe or regular follow commands.

I've seen a lot of people post issues with Jamba Strobe, since 3.3.
Not sure if there was a change in Jamba.
Or if it is a change to the Blizzard API for follow.
So far the threads are in regards to IS Boxer and Keyclone here.
As well as PB (the software we're not supposed to mention) on their site.
With it affecting three different boxing options, I'd tend to think it is software independent.
But not really sure of a fix.
I do plan on 5x melee Worgen in Cataclysm, so a fix would be wonderful.