This would be my approach...
1) First create an event receiver as given in below code. This code will make "Check In Comments" field mandatory. Check In Comment is the multi-line textbox that appear when you are trying to check-in a file in a library.
public class EventReceiver1 : SPItemEventReceiver
public override void ItemCheckingIn(SPItemEventProperties properties)
string comment =
properties.ErrorMessage = "Comment Empty";
properties.Cancel = true;
2) Download custom SPD Workflow Activity - Start Another Workflow and install it on SharePoint Server .
3) Create a workflow where you should a put a condition - Wait for Check In Comment to be not empty and just right after this condition insert the custom action Start Another Workflow.
In all you must create two workflows. One is your actual workflow and the other is the triggering workflow that contains step 3.
Hope this helps.