Load flat file data to SQL - when calling from a job, no or few records commit without error, when running manually from solution, it works

Question

I'm perplexed and would appreciate any help. My SQL setup works by jobs running throughout the day that will upload flat file information if the flat file exists. This is setup using variables and loops and 90% of the jobs run without issue daily.

About six weeks ago, we changed where our flat files were being saved and this caused issues with the formatting that required me to rewrite many of the flat file managers to ensure all records worked correctly. This has been resolved and works perfectly when I'm running all of these jobs manually through Visual Studio.

Now, when a handful of these packages are called from the SQL job, they either do not write any records, or only write a handful of them, and no error is thrown. When I go back into Visual Studio and run them manually, they work without error.

Details on two of the flat files:

1. SHIPPED.TXT - size: 2.13 MB; 2,342 rows; rows committed when loading from SQL job: 85
2. WIP.TXT - size: 11.3 MB; 29,479 rows; rows committed when loading from SQL job: 11,057

I have tried turning off fast load, reorganizing the order they are called in the SQL jobs, thinning out the SQL jobs when they are called, all to no avail.

I'm stuck. Has anyone ever experienced anything like this before?