When you are in the transport connection and select via filter some transformations, some or all of them do not appear in the selection result.
If that occurs to you, check the button “Source System Assignment” as in the image below and make sure you have selected all systems for which you are selecting transformations. This info is contained in table RSOPROPERTIESTAB, enter your user and as property enter “PROP_SOURCE_SYSTEM_SEL”.
Your post saved me from going crazy!!