I have looked into the record counting (i was mistaken as there used to be a record count displayed for each base node, this was removed previously removed) , when you switch files on the Datasource tab of the importer, this is the xml file being pre processed / indexed to allow for quicker interaction using the visual data selector and base node selector, this is required when a file or new file is selected for these to work.
If it is crashing your server could you please send me an a copy of your php error log so i can help resolve this issue, the file indexing/processing has been optimised to have a low memory footprint using file streaming.
In the mean time i will look into custom field list not populating, i have noticed that there is some delay in the custom field list populating, does sthis sound like the same issue? If you check the" enable text field" for that custom field does the custom field key appear? Are you using "Advanced custom fields", or some similar plugin for your custom fields?