This is very strange, I've never had troubles depositing BTC into BTC-e. I would keep sending them tickets, maybe even post in trollbox because if it is as you say it is unacceptable
my first deposit of 0.98btc wasn't a problem. Take a look at my block chain transaction
https://blockchain.info/tx/89a51ea735bca437e014e4536974eb442f57900d3fe1d6fbc13d70bc9ca29cedAnd on my btc-e bitcoin deposit page I see the transaction as uncommitted and 0 confirmations.