As I explained here http://forum.cellprofiler.org/t/failure-to-load-ome-tiff-sample-data/4317/3
You may try :
First open your image in ImageJ, choose "Image" > "Properties" > make sure it is set with Channel (c) = 2, slices (z) = 3
Even though you may see it is already set so, please save the image as new anyway (as .tif)
Then load the newly saved image. Open it in CellProfiler.
In Module "Metadata" > "Extract metadata" from "Image file headers" > Update the field.
Now you would see the channel and slices are shown correctly.
Note: Python indexing starts from 0
For multiple images, you can do batch process in ImageJ (basically: open and re-save as new files with correct properties).
Hope that helps.