I am using a Linux computer. The issue I am having is that sometimes I have to use "kill -s 9 (bitcoind pid)" and restart bitcoind using "bitcoind -txindex" because bitcoind will sometimes not let me use "bitcoind stop". For example:

brian@brians-lair3:~/Desktop/VH2_apache2/host02/btc15$ bitcoind stop
error: incorrect rpcuser or rpcpassword (authorization failed)

This happens after bitcoind has been running for a few hours or so. It also locks me out of bitcoin-cli:

brian@brians-lair3:~/Desktop/VH2_apache2/host02/btc15$ bitcoin-cli getinfo -rpcuser=b -rpcpassword=a
error: incorrect rpcuser or rpcpassword (authorization failed)
brian@brians-lair3:~/Desktop/VH2_apache2/host02/btc15$ bitcoin-cli getinfo
error: incorrect rpcuser or rpcpassword (authorization failed)

Even when I specify the correct password and username it doesn't work. Initially when I start bitcoind though, I can use bitcoin-cli:

brian@brians-lair3:~/Downloads/DownloadsArchive$ bitcoin-cli getinfo
{
    "version" : 90300,
    "protocolversion" : 70002,
    "walletversion" : 60000,
    "balance" : 0.00000000,
    "blocks" : 352549,
    "timeoffset" : -1,
    "connections" : 26,
    "proxy" : "",
    "difficulty" : 49446390688.24143982,
    "testnet" : false,
    "keypoololdest" : 1421427760,
    "keypoolsize" : 101,
    "unlocked_until" : 0,
    "paytxfee" : 0.00000000,
    "relayfee" : 0.00001000,
    "errors" : ""
}

Also here is my bitcoin.conf:

rpcuser=b
rpcpassword=a
txindex=1
server=1

here is debug.log, its at this link:

1. goto 66.42.220.205:18809 (its a website) type that in URL box 
in a web browser

2. download debug.log

My question is can I prevent bitcoind from eventually coming to a point where I have to restart it using the command "kill -s 9 (pid)" and "bitcoind -txindex", or can I prevent it from coming into a state where it wont let me interact with it? If I can prevent this, how do I?

Also I need to use -txindex because it keeps an index of transactions and I need that for payment processing.

Thanks in advance!