Hello,   
i have got exactly the same issues after the last updates. Any solutions? I have already removed and re-installed the BF-109 in DCS World final and beta. 
But this does not work for me!   
If i remeber correctly, the damage model of the cowlings was tweaked. I think since then i have got this problems.   
By the ways all other modules seem to work fine so far! 
With kind regards!