See the definition 7 from this dictionary:
- 加重语气,有“的确”、“实在”的意思:天气~冷。
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:
A: 今天天气很冷!
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.