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.
* The minimum amount of deposit - 0.0001 BTC.
* Enrolment takes place within 1 minute after the 3 confirmation of the transaction in the network.
* Commission for deposit will not be charged.
* Address can be used for next deposits.
Deposit BTC
Your address for deposit BTC:
1MJ9goaZtMgGPDbtLKVa616j3njxXdszUk
Generate new address
Uncommitted transactions:
+7.92850980 BTC, 0 confirmations, 03:28 15.05.13
Note: The information is updated every minute.