As Wayfaring Stranger pointed out in the comments, ticking over means "continuing to work".
Just about ticking over means "almost ticking over" or "very close to ticking over". The phrase carries a connotation of anticipation; it implies that the company may be ticking over in the near future.
Only just ticking over actually has two possible meanings: "barely ticking over"1 and "recently ticking over"2. The first meaning has a more pessimistic connotation: the company is ticking over, but it could be doing a lot better, and it could stop ticking over at any time. The second meaning is more neutral; it's just a statement about when something happened.
Which situation is "better" depends on which meaning of only just you pick, as well as your expectations for the future.