This problem 100% nothing to do with CleanMart. I can tell you that. Did you try investigating this problem via forum.virtuemart.net?
Apparently your server is having problem with generating the PDF invoice upon order status change, because this is what tcpdf.php does..
The first thing you should do is; upgrade:
Virtuemart to com_virtuemart.3.2.6
Virtuemart AIO to com_virtuemart.3.2.6_ext_aio
TCPDF to com_tcpdf_1.0.4
(you can get the installation files for these new versions when you download the Virtuemart ZIP package from
virtuemart.net/download)
Upgrading (especially upgrading tcpdf) might resolve the problem you get. By the way, I don't see any relation between that error message and SEF though. I can't be sure why this happens only when SEF is on. I believe it is always problematic, but it causes "fatal error" only when SEF is on. That is my guess.
Just to be sure that, this problem has nothing to do with our template. You can temporarily disable CleanMArt and try again.
To temporarily disable CleanMart, follow these 2 steps:
1- Rename this folder:
/template/YOUR_TEMPLATE/html/com_virtuemart/ to
/template/YOUR_TEMPLATE/html/com_virtuemart2/
2- Unpublished this plugin: "Flexible VM3 Template"
Once you do these 2 simple steps, you will notice, CleanMart will be completely eliminated from your Virtuemart Pages. Please try it, and you will keep getting the same error messages. Nothing will be changed.
Regards.