I really don't understand what you mean exactly. Can you be more precise with examples please. Did you check this issue on older versions, so you can confirm that this issue has something to do with an version update or newer Vicibox? Are you sure these callbacks you are talking about were saved as "useronly"? There are a bunch of campaign settings and also user override settings, which can affect a mismatch of count. For example these campaign settings:
Scheduled Callbacks Count -These options allows you to limit the viewable callbacks in the agent callback alert section on the agent screen, to only LIVE callbacks. LIVE callbacks are user-only scheduled callbacks that have hit their trigger date and time. ACTIVE call backs are user-only callbacks that are active in the system but have not yet triggered. You can view both ACTIVE and LIVE callbacks by selecting ALL_ACTIVE. Default is ALL_ACTIVE.
Scheduled Callbacks Hours Block -This option allows you to restrict a USERONLY scheduled callback from being displayed on the agent callback list until X hours after it has been set. Default is 0 for no block.
Scheduled Callbacks Active Limit -This option if enabled will limit an agent to this number of active or live user-only callbacks. If the limit is reached, the agent will not be able to select the My Callback checkbox when setting a callback for a lead. Default is 0 for disabled.
Vicibox 6.0.2 from Vicibox_v.6.0.x86_64-6.0.2.iso | Vicidial 2.12-560a build: 160617-1427 | Asterisk 1.8.32.3