Hi,
It sounds like the server is overloaded, and can't cope with the extra load of performing a backup. Presumably other uses of the server, other than your website, have been increasing over time - you'd need to speak to the webserver admin about this. Lowering the 'split' limit has the largest effect of anything on resources (the lower the split, the lower the resources needed), so this ties in with that.
- the popen / zip error
This just means that use of the PHP popen() function is not allowed on the server. That's not problematic - UD has 3 different zip engines, and if one can't be used, it moves on to the next.
UD uses WP's cron system - so, if the scheduled task seems not to have run, then the best way to investigate is by looking at your list of scheduled tasks with a plugin like WP-Crontrol.
David