Been a while since I read Steven Newton's
Joseph E Johnston and the Defense of Richmond - which is one of few, if not the only, in depth assessments of the Confederate war effort in Virginia pre-Lee assuming command
- but I seem to recall that there was a lot of petty power plays between the Confederate Army and the new Confederate Government, and as Benjamin was Secretary of War this put him in the direct line of conflict with Joe Johnston.
Looking through it now, Newton has a index subjected under Benjamin's name titled "Quarrels with Johnston, the largest section of which explains that Benjamin was party to considerable interferance in the affairs of Johnston's army, with this cited as "the most egregious outrage":
...the unceasing campaign by Secretary Benjamin to undermine the general's command authority. The Louisianian ruled the War Department as if it were a personal fifedom. He sent orders directly to Johnston's subordinates without consulation or even informing the general. He first acknowledged, then arbitrarily repudiated Johnston's organization of the army into two corps. Benjamin fostered a climate at the War Office that made it acceptable for everyone, from the lowest private to a general officer, to send him requests without channeling them through the department commander. More often than not, even when official papers passed through Johnston's hands, Benjamin would overrule his decision in an apparent matter of course. Much of Johnston's trouble eradicating alcoholism among his officers could be traced to Benjamin's refusal to implement the recommendations of Johnston's courts-martial...
...At the same time, Benjamin undercut Johnston's furlogh and reenlistment program by granting authorization to dozens of recruiters to move among Johnston's camps to try to entice unhappy infantrymen into signing up for new companies of artillery or cavalry. These recruiters arrived armed with furloughs approved by the secretary of war, which Johnston possessed no power to contravene. Johnston...confrontd Benjamin on this issue, pointing out: "You will readily percieve that while you are granting furloughs on such a scale at Richmond I cannot safely grant them at all."...
Benjamin denied that he had ever acted so improperly, even though the most superficial glance at the letterbooks of the War Department would have proven him a liar. Following this exchange, D.H. Hill forwarded a sheaf of authorizations signed by Benjamin to General Coopeer, with the sarcastic request: "Will you be kind enough, General, to forward this note to the Hon. J.P Benjamin that he may be advised that there is a forger in his office."...
...Eventually, Johnston brought his complaints to the attention of Jefferson Davis. Instead of inspecting the evidence, Davis simply asked Benjamin for an explanation. The secretary's response was a collection of misleading - if technically correct - statements, facile half-truth, and outright falsehoods, tied together by his lawyer's charisma into a rationalization that a close friend could find acceptable. Johnston, in fact, came out of the exchanged with a mild rebuke. Davis observing that Benjamin "has complained that his orders are not executed, and I regret that he was able to present to me...many instances to justify that complaint."
Newton: pages 21 and 22
Bringing the