HI
I agree you are leaving your pup for a perfectly acceptable amount of time.
I wonder if before this, you had spent all the time with the pup and then suddenly left for 30 mins to an hour?
As the pup may, (possibly, just a suggestion) be slighty anxious because of the mess. Please dont be worried though as i may be wrong, i am looking at the worst scenario.
If you use a crate, introduce it very slowly or it will make pup more anxious, once used to a crate they do feel safe

(well, usually!).
Have you tried leaving the pup for say 3 minutes to walk up and down the road, then 5, then 8, then 10 - over a period of weeks. I did this with my pup, her breed hates being left but she is great now at 13 months and can be left if necessary for up to 4 hours. (RArely happens but it's useful to know she is able to cope).
Use a child gate at home to get pup used to not being with you all the time.
Try to get hold of a book callled The Perfect Puppy from www.crosskeysbooks.com, it gives loads of help about this sort of thing.
Good luck

lIndsay