With the new timetable many trains are given more generous turnbacks at Frankston as both platforms are used when possible. Previously only platform 1 was used most of the time with typically 8 minute turnbacks meaning a train arriving more than a couple of minutes late would be much less likely to return on time given the driver may need a toilet break and has to walk to the opposite end anyway. Late arrivals now return to the City punctually more often.
Although this is the case on weekdays, the changes to the weekend timetable in June saw the turnaround time cut from to 14 mins to 8 minutes.
This means if a train is more than 6 minutes late arriving from the city, it results in the return Up train departing Frankston late. With the likely minor delays enroute back into town, not surprising that many weekend trains are failing to meet the stricter 4:59 performance benchmark.
When track work takes place on the Frankston line the advertised connections do not apply; in general you need to leave the City 20 - 30 minutes earlier to maintain your connection. This fact is advertised in advance.
A standby bus is provided at Frankston during trackworks for those who miss their connecting train. This has been the case for over 5 years now - once I even rode a Ventura bus down to Stony Point on one of these standby services.