Property Checkpoints failling on TestExecute, but running OK on TestComplete (TE and TC 8.7)

You wrote that you disabled IE setting to create separate processes for opened web pages. Did you do the same thing on the computer where TestExecute works? If yes, then I think you should make sure that there are no running IE processes when test starts or write some code to enumerate existing IE processes and find the needed one by its Page child node (comparing the page URL).