When Stitch loads a house for the first time, all folders (floors and rooms within floors) are sorted by folder modification time and that order is then remembered by Stitch. Normally that results in rooms shown in the order in which they were shot. If you do any fisheye image editing in external software, that may change folder modification time when you save edited images back to disk and depending on how your image editing software works, it may affect the sorting order. You would need to check how your software is configured (order in which it saves to disk).
You could first load a house in Stitch, then edit fisheye images. When you load house in Stitch, it will use existing fisheye images for a) alignment, which should not be affected by color changes or photoshopping and b) producing the preview pano (photosphere) that is shown in Stitch main window for each room and that image will not reflect you color editing done outside of Stitch after that image is created. But that image is not used in iGuide and is only shown in Stitch and our drafting software. If you want to update those preview images, you could search house folder for t.pic files, delete them all and then reload the house.