The Victorian government has removed a bunch of level crossings, but with the underground stations this tends to cause a loss of coverage.
I've noticed this at stations such as Ormond, McKinnon, and Bentleigh in particular.
I'm also on the Frankston line and you are right. When passing through the stations that have undergone redevelopment, there's been a noticeable loss in signal strength.
Given the design of the stations you've mentioned (which are now underground, reducing your line of site to your closest mobile tower), there are also more physical obstructions to contend with i.e. dense concrete walls.
Not a perfect solution, but temporarily switching to 3G could make a difference. The 3G network on a frequency range. Typically, the higher the frequency, the better the penetration, and less signal loss.