Does having Default Database Engine MyISAM and keeping InnoDB tags in my.ini create any problem?
Binary Logs
As for your binary logs, the bad magic number is making reference to an encoding done at the beginning of the a binary log. It is a base64 constant that looks something like : 0xfe 0x62 0x69 0x6e. This is referred to the binlog magic number. If this encoding is not in this format, it would be reported as corrupt.
You should erase all binary logs and start fresh.
In order to clear them, run this in the mysql client
mysql&gt; RESET MASTER;
mysql&gt; SHOW MASTER STATUS;

This will erase all binary logs and show you the first binary log.
I have written posts on this issue before

Oct 28, 2012 : Binlog has bad magic number
Dec 26, 2011 : mysql emits BINLOG rows even though binlog_&#173;format=&#173;STATEMENT

InnoDB Options
It is OK for the InnoDB options to be around. Keep in mind that every time mysql is restarted, InnoDB's infrastructure is validated

mobiledoc_InnoDb_data1 exist in the innodb_data_file_path (D:/eClinicalWorks/mysql/data)
mobiledoc_InnoDb_data1 must be at least 300M
innodb_data_home_dir has ib_logfile0/ib_logfile1
innodb_log_file_size=256M (checks if ib_logfile0/ib_logfile1 are 256M)
innodb_buffer_pool_size=256M (allocates the 256M in RAM)
innodb_log_buffer_size=8M (allocates the 8M in RAM)

If none of your tables are InnoDB but you want to keep the present InnoDB settings and corresponding files, I have a great suggestion:
Add this under the [mysqld] section of my.ini
[mysqld]
skip-innodb

then run
C:\&gt; net stop mysql
C:\&gt; net start mysql

This will make mysqld startup faster because all the steps for InnoDB initialization/validation are bypassed. The memory InnoDB is configured to use (264M [256 + 8]) will not be allocated.
Give it a Try !!!