sounds like a combo of things.
teething and separation anxieties and some go through phases of not liking the cot.
I think a Dr check would ease you of any physical worries.
some white noise may help too.
dd has always had issues with the cot, she hated being stuck in there. so we have her cot sidecar to our bed and alittle lower then our bed, but for your young one the same height may be better.
we have a routine for sleep. every sleep. a book, a song then kiss and cuddle then in a firm voice I tell her its time to sleep, sweet dreams. and now she knows what's happening and what's expected. (dd is 15mth)
I hope you can find a solution.
teething can.be an awful time