A scheduled job works so that each site connected to the database will setup a timer for the job. The job will only execute on the site that the timer is first fired on.
So my thought is that can it be that you have some other site (test, staging etc.) that is connected to the same database. And perhaps some assembly is missing on that site?
However when you run the job manually it should execute on the site you currently are logged into...
We have a scheduled job that runs on one minute interval. However, we have noticed that it randomly fails. On the history page it just shows 'FAILED. Could not load file or assembly 'myassembly' or one of its dependencies. The system cannot find the file specified.'. The issue also occurs sometimes when the job is activated manually or when the job is set at a longer pace so it is guaranteed to finish it's work (we thought that this was the problem at first). This happens on our different environments also.
Any help appreciated. I've not found anything in EpiServer or the application logs. I guess the exception comes from somewhere deeper in EpiServer but maybe we've missed something on our job implementation also.