This was not really a API-developers question, so I moved the topic into the general section...
If I understand you well, my wild guess is that the gaps between every subtitle sequence is not large enough, maybe 1 ms or even 0.
VLC is pretty flexible, it will even take subs with gaps of 0 ms. But I would recommend a technical minimum of 50 ms. More 'beautiful' is gaps of at least 125-170 ms (or rather: 3-4 frames)
For example, here the gap is 125 ms:
00:01:04,425 --> 00:01:07,000
The first subtitle sequence.
00:01:07,125 --> 00:01:09,600
And here is line number two.