The first Woocommerce issue was likely unrelated to ACF Pro.
The latter two popped up because acf_form_post::save_post() hooks onto ‘save_post’. This hook only fires if something changs on the post’s <i>main</i> fields. What this means, for example, if you change a field within an ACF metabox without changing anything else, this hook doesn’t fire. Instead, hook into ‘pre_update_post’. See this diff to solve this problem:
http://pastie.org/9617141
Here is a reference to this same problem in another plugin.
