Agents are not calls. Thus "Agent Logs" and "Call Logs" will not match up.
Not all calls are in any way related to an agent. Agents can be associated with lots of calls or no calls. The timing involved in calls are therefore not related directly to individual or groups of agents.
Trying to reconcile them will never work. This basic fact is actually why Vicidial exists: The goal here is for the Dialer to manage the calls that would otherwise Waste Agent Time.
For example: If an agent logs in with the dialer set to 100:1 call ratio, then logs right out immediately without waiting for any calls to answer ... the agent would have 2-10 seconds of "time" in a log somewhere. But those 100 calls would all get dialed and all have their own logs that are in no way related to the agent who is now "logged out" and unavailable, thus NOT linked to any of these calls. Some may answer, others would not ... plenty of log entries related to how long the answered calls may have lasted and/or rung. AMD may or may not become involved (more logs!). If the campaign in question plays a recorded message, that message may or may not have played (lots more logs!) ... but NO agent time was ever involved in any of those calls.
With that basic precept, it follows that agent logs and call logs will never "align".