There is a known issue in Windows, that when you push a large file to another server all the memory ends up getting allocated to the System cache instead of the user processes. You can look in the Physical Memory (MB) section of task manager to see how much memory is allocated to the system cache.

This can be solved by backing up to a local disk, then having the remote machine pull that file.

STEP #1

Set innodb_file_per_table to 0 in /etc/my.cnf

[mysqld]
innodb_file_per_table = 0

STEP #2

service mysql restart

STEP #3

Convert every InnoDB table to InnoDB again

echo "SET SQL_LOG_BIN = 0;" > /root/ConvertInnoDBToInnoDB.sql
MYSQL_CONN="-u... -p..."
SQL="SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=InnoDB;')"
SQL="${SQL} FROM information_schema.tables WHERE engine='InnoDB'"
mysql ${MYSQL_CONN} -AN -e"${SQL}" >> /root/ConvertInnoDBToInnoDB.sql
less /root/ConvertInnoDBToInnoDB.sql

Once you view he script and are satisfied, login to mysql and run this

mysql> source /root/ConvertInnoDBToInnoDB.sql

EPILOGUE

All .ibd files will vanish and all InnoDB tables and indexes will exist inside ibdata1

Give it a Try !!!