How is 是 in these two sentences?
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.