See the definition 7 from this dictionary:
天气冷 vs 天气是冷, the latter means that the truth is that the weather is cold, 天气确实/的确冷. The former just means the weather is cold.
In practice, 天气是冷 is used to confirm/justify what the other person have said. 天气是冷 stands alone (without previous contexts) doesn't make much sense. Refer to this exchange:
B: 恩，今天天气是冷！ // implying B agrees what A have just said by repeating it with 是 for emphasis.
Back to your examples, 你是在说 means what you are actually saying is...., while 你在说 is what you are saying is.... 我不是很懂你的意思: I don't really quite get what you meant. 我不懂你的意思: I don't get what you meant.