English Translation
I’m not sure what you were thinking.
être certain in negative statements is supposed to be followed by the subjunctive, right?
Pensiez then would be present subjunctive, so should the translation be:
I’m not sure what you are thinking.
past subjunctive would be: Je ne suis pas certain de ce que vous pensassiez.
I’m not sure what you were thinking.
I am not a native French speaker, so just trying to figure this out. Thank you in advance.
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It’s my understanding that in modern French the present-tense subjunctive has taken over the function of the past subjunctive, which is no longer in use.
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I found an interesting debate online about whether French subjunctive was being used at all anymore! Thanks for the answer.
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First time I see the word “pensassiez”.
Thanks ! 
Also…
To me the English sentence sounds like a nicer version of “What [insert colorful words here possibly] were you thinking!”, but maybe that’s just me, so I thought I would ask:
When you use “I’m not sure what you were thinking.” in English, is it neutral? I mean, doesn’t it often imply that you are displeased or unhappy on some level?
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It certainly could be said like that (like you idiot!).
It could also be said like, I don’t know what you were thinking…
-when you bought that piece of land by the river 30 years ago, but it was a great idea!
-when you asked what I want for my birthday, but I want a new car!
It could be anything that surprised or might surprise somebody else. So it is totally by context.
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That’s interesting…
I feel like the “you idiot!” version is much more common, but I guess it’s just confirmation bias on my part.
Probably says a lot about the kind of stuff I read/watch too. Oh well… 
Thanks for clearing things up, @corgwin24 !
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I’m British and to me that phrase is definitely of the “you idiot!” variety.
I would say that in increasing levels of frustration, one might say something like -
- “Well, that’s one way to approach the problem.”
- “That’s not exactly what I had in mind.”
- “I’m not sure what you were thinking.”
All of these typically mean “What on Earth have you done !”.
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Maybe the negative is more common. (The next line from the other person would be “Hindsight’s 20/20“.)
I’ve said it to myself a few times LOL. (I don’t what I was thinking.)
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This one made me laugh ! 
Yes, pretty much how I feel about these as well 
Really interesting stuff anyway, and next time someone says that to me, I’ll try not to assume they’re calling me an idiot, albeit very politely…
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I will make one last explanation for neutral. The original sentence is: I’m not sure what you were thinking.
You hire someone to landscape your yard and they come out to look at it. They might well start by asking: I’m not sure what you were thinking.
I don’t really like it very much if someone asks in a not-neutral way: What in the world were you thinking?
I agree, really interesting. These discussions are what make clozemaster work for me.
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I agree “I am not sure what you were thinking” often insinuates “you idiot.” However, I can definitely see neutral situations such as:
“I don’t know what you were thinking but I would like to suggest going to a movie” (=I don’t know what you had in mind, with emphasis on “you”)
A different topic regarding this sentence - I would not have thought to use subjunctive because it is not Je ne suis pas certain que … but instead de ce que ___________. To me, the main sentence is Je ne suis pas certain de (objective of “de”). And “ce que …” is the objective of the preposition de. I know subjunctive can be used “dont” but do the same rule apply to the dependent sentence following “ce que” serving as object of the preposition?
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So I shouldn’t automatically assume that what he is really saying is: I’m not sure what you were thinking… when you bought this piece of crap, you idiot! - Alright then 
Right, that’s what I got from @corgwin24’s example as well. I think I would typically use “what you had in mind” in similar cases.
Absolutely.
I have to say that this sentence does sound weird to me. It is grammatical, but it just sounds a bit off. I feel like we wouldn’t really say that. It may well be because of the "je ne suis pas certain de ce que". construction.
Je ne suis pas certain que is very commonly used however.
With all that said, I’m having a hard time coming up with a translation that I actually like…
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