A checkpoint can only be taken at the completion of calculation for a structure. The work units contain different numbers of structures in an attempt to have a consistent run time for each work unit. I have seen work units with over 20 structures but some have only one. A work unit with only one structure will run for 2 hours without a checkpoint. This is the reason your work units return to 0% completion after a shutdown.

On my PC many MIP units tend to have a calculation error if my PC is shutdown and rebooted. In order to overcome this problem (and would also solve yours) is to hibernate the PC instead of shutting it down.

Have you checked in the Result Status on the website to check if this is also happening to you? Also in the Result Status section of the website in the text output for your work unit there is a parameter 'nstruct' which I deduce is the number of structures in the work unit. This can also be seen while the work unit is running in the stderr.txt file in the slot folder for the executing work unit.

When I hibernate my current PC, the state of the running machine is written to the hard drive, the PC appears to close down completely and I am able to switch off the electrical power at the socket.
On my previous PC after hibernating it appeared to be closed down except for one flashing LED. I also had to leave the electrical power switched on at the socket but I think it consumed minimal power.

madmac: under the tasks tab, click on one of the running WUs and then click "properties". This will tell you the last time the WU checkpointed.

If the WU is showing a 20%, 40% or 60% completion figure then it almost certainly won't have. I've just swapped to SCC full time, but in the last week or so I started to download a small number of SCC tasks to switch to before shutoff time (by manually suspending Ready To Run MIP tasks before the current MIP tasks finished).