Mk1 Lander Can - Strange things happening

[Epthelyn]

As a result of whatever crazy stuff happens when you stop timewarp with ASAS enabled when attached to an asteroid, I now have a PPD-12 Cupola Module orbiting Kerbin between 2.9Mm and 83Mm. Inside is one Kerbal.

The only chance of a rescue would be to either rendezvous with it and pass the Kerbal over into a spare pod or to use the Advanced Grabbing Unit. Obviously the latter is the more appropriate given the recent update and its introduction.

Since it's only a to-orbit-and-back mission I figured I'd use a 1m craft, and make use of the Mk1 Lander Can because the flat top (if you don't know the name, it's the 1m octagonal grey thing) is a nice place to put the AGU.

I threw something together fairly quickly, put it on the pad and warped forward a couple of hours to give the orbit of the stranded Kerbal time to pass over KSC; I could then launch northwest and save on a plane change later on.

After warping something weird happened. I fired up the engines and the rocket disintegrated for no apparent reason, leaving only the Lander Can suspended about 40 metres above the launchpad. This can be reproduced:

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As a result of this I decided to forgo the waiting and do the plane change in orbit. I launched into a west-facing equatorial orbit and warped forward to circularize. When the timewarp stopped, a similar thing to what happened in the first picture in the imgur album happened; the pod remained stationary and the rest of the rocket bent round it - The second stage 3.75m tank ended up destroying the pod as it collided.

After modifying the rocket to use the mk1 pod (black circular thing) instead this does not happen, and I can't reproduce it with any other pod.

The only mod part involved is the Kerbal Engineering System & Flight Engineer, but the issue still happens with that removed and I've had that on every rocket I've launched since I downloaded .23.5 on release day.

In summary: If I warp with a Mk1 Lander Can attached to my rocket, it appears to fix in position and stay there.

What's going on?