FINALLY!!! I just had an excellent CS chat session that ended up with getting this actual issue addressed!

Here's what to do:

1. When you create an invoice, go into the DESIGN tab on the right hand side.

2. Under OTHER TEMPLATES, select PROGRESS INVOICING OPTIMIZED...

3. If you have another template marked as default, de-select it as default.

Your logo should now appear normal on the invoicing email.  This is a brand new update apparently, so somebody must've been listening somewhere.  I hope this helps out others.  Good luck!