The Miche cranks are ISO, you've rammed them onto a JIS taper Shimano BB, if the chainline is now different when going back to the Miche I'm afraid to say it sounds like you have distorted the tapers on the cranks when you used the Shimano BB - ISO and JIS are not really meant to be mixed - you can do it, I've done it myself (with cheap cranks!), but there is always the risk that permanent changes to the crank tapers will result... I very much doubt there is anything wrong with the frame, it would have to be bent like a banana for that amount of difference at the chainstay result!
The Miche cranks are ISO, you've rammed them onto a JIS taper Shimano BB, if the chainline is now different when going back to the Miche I'm afraid to say it sounds like you have distorted the tapers on the cranks when you used the Shimano BB - ISO and JIS are not really meant to be mixed - you can do it, I've done it myself (with cheap cranks!), but there is always the risk that permanent changes to the crank tapers will result... I very much doubt there is anything wrong with the frame, it would have to be bent like a banana for that amount of difference at the chainstay result!