Having a similar issue with Jigoshop and WooCommerce (latest versions, on PL 2.4.4 on WP3.6)...
Jigoshop suffers from not being able to install the PL adapter plugin (this I guess is a Store issue...FATAL ERROR etc on attempt to install the plugin via store).
WooCommerce...the PL plugin installs OK but I still get the same issue – Pagelines loses all control of the Shop page, which seems locked at a default setting for whatever template is set for it.
I.e. none of the PL metasettings work for the shop page..even the Page Options... i.e. Pagelines retains the state of checkboxes and fields, but there is no effect on the outputted page.
Should I try either of the methods listed on the WooCommerce site: