I've met the same problem.
The only way I've found is to redefine the function that handles that part of the export and to put it as a emacs-lisp source block at the beginning of my org file.
Here is what I did:
(defun org-latex--caption/label-string (element info)
"Return caption and label LaTeX string for ELEMENT.
INFO is a plist holding contextual ...
TeX-run-compile runs the make process not in the current buffer but in the *compilation* buffer.
That is the reason why TeX-command-sequence does not find the running make process. It cannot set its sentinel for the make process. That sentinel would start the next command in the command sequence.
Use TeX-run-TeX instead of TeX-run-compile. With TeX-run-TeX ...