We can try rebuilding the BCD. But pre-boot shouldn't take that much time. If it can't find the BCD or boot files, it usually shows an error message right away. However, it's like trying hard to find the storage device or enumerate some other peripheral during the pre-boot phase.
Secondly, if the boot files are corrupt, the problem will be consistent; it can't be erratic, based on my experience.
Please post a screenshot of Disk Management. Also, post the output of these commands from an admin Command Prompt.
bcdedit
diskpart
list disk
list vol