Suppose we have two sentences, one in the indicative mood:
If the train was leaving, you would have heard about it.
and the other in the subjunctive:
If the train were leaving, you would have heard about it.
What is the key difference in meaning? Am I right to guess that in the first sentence the speaker is unaware of whether the train was indeed leaving, whereas in the second sentence he knows that the train was not leaving?
The subjunctive mood is quite rare in modern English, or you can say that in many cases it has evolved to overlap with the indicative. The second sentence you are giving is one of the remaining forms, in the second conditional we use "were" for first and third person singular, instead of the indicative "was".
The other example has the exact same meaning. The difference is that, strictly speaking, it is grammatically incorrect. However, there seems to be a strong tendency among native speakers to use "was" instead of "were" in this case, since in any other case we say "I was" and "he was".
And to answer your question, there is no difference in meaning, only two forms for the same thing, one of which is "grammatically correct", and the other - more and more popular, and, in my opinion, soon to be seen as "grammatically correct".
The short answer is both sentences have the same meaning. I would say that usage is the only difference. Although "if it was" is regarded as incorrect, this ngram indicates the use of the more acceptable "if it were" is declining (perhaps because it is seen as formal).
The longer answer is more interesting and it tells us about the subjunctive mood in Old English.
The first question that rises is what we mean by subjunctive mood. Since we are at ELL, I will try to keep this answer simple while crossing my fingers to not start a flame war :). So... a verb can be classified by different criteria, for example:
tense (past, present, future): depending on the time when the action/event described by the verb takes place.
aspect (perfect, continuous, perfect continuous, simple): without going into details, just say, the aspect of a verb describes the action/event further (is the action/event happening before another event/action? is it a continuous action? is it a continuous action that happened before another even/action? is it none of the previous?)
mood (indicative, subjunctive, imperative)
The indicative mood is the mood used most often, because is the mood we use for actions/events that happened, are happening or will happen.
The subjunctive mood, however, is used for actions/events that didn't happen but could've, or actions/events that won't happen but could.
Here's the most important point in this answer: how can we express the subjunctive mood in English? As often happens, the answer to this question evolves with history.
Old English had more forms to express the subjunctive mood than modern English. This doesn't mean that modern English cannot express the subjunctive mood. It means that:
the forms used in Old English are in decline and are often regarded as too formal.
alternative forms are created in modern English: the use of past tenses, the use of would, should...:
it is essential that the state should have no hand in regulating the press
it would be better if they would tell everybody in advance
some of old forms still remain:
were: I wish it were Summer
be: a Florida judge has recommended that he be allowed to work
other infinitive forms: God save the Queen
if they would tell is actually subjunctive, only it would be better is conditional.
Fortunately, it's simpler than that. There is no difference in meaning, just in usage. "Were" is more correct when invoking this particular conditional case (I believe it's called the subjunctive case). It's common to hear it the other way, depending on where you are, but it it's never correct. You'll want to say "If the train were leaving, you would have heard about it."
