Metabox saving values

First, you don’t need the <form> tags; meta boxes are already rendered inside the post edit form.

Second, if a checkbox is not checked it is not sent, so isset( $_POST['checkbox_name'] ) return false and the custom field that stores the value of the checkbox is not update correctly.

I’ve tested this code with standard post type and it works, it must works also if you use it with your custom post type:

function kvkoolitus_prices_metabox() {
    add_meta_box( 
        'kvkoolitus_prices_metabox', 
        __( 'Course Price', 'kvkoolitus'), 
        'kvkoolitus_prices_metabox_callback', 
        'post', 
        'normal', 
        'default'
    );
}
add_action( 'add_meta_boxes', 'kvkoolitus_prices_metabox' );

function kvkoolitus_dates_metabox() {
    add_meta_box( 
        'kvkoolitus_dates_metabox', 
        __( 'Course Time', 'kvkoolitus'), 
        'kvkoolitus_dates_metabox_callback', 
        'post', 
        'normal', 
        'default'
    ); 
}
add_action( 'add_meta_boxes', 'kvkoolitus_dates_metabox' );

function kvkoolitus_dates_metabox_callback( $post ) { 

    wp_nonce_field( 'kvkoolitus_dates_metabox_nonce', 'kvkoolitus_dates_nonce' ); ?>

  <?php         
    $start_date = get_post_meta( $post->ID, 'kvkoolitus-start', true );
    $end_date   = get_post_meta( $post->ID, 'kvkoolitus-end', true );
    $duration   = get_post_meta( $post->ID, 'kvkoolitus-duration', true );
  ?>

  <p>   
    <label for="kvkoolitus_start_date"><?php _e('Start date', 'kvkoolitus' ); ?></label><br/>    
    <input type="text" class="widefat kvkoolitusDate" name="kvkoolitus_start_date" value="<?php echo esc_attr( $start_date ); ?>" />
  </p>

  <p>
  <label for="kvkoolitus_end_date"><?php _e('End date', 'kvkoolitus' ); ?></label><br/> 
  <input type="text" class="widefat kvkoolitusDate" name="kvkoolitus_end_date" value="<?php echo esc_attr( $end_date ); ?>" />
  </p>    

  <p>
  <label for="kvkoolitus_duration"><?php _e('Duration', 'kvkoolitus' ); ?></label><br/> 
  <input type="text" class="widefat" name="kvkoolitus_duration" value="<?php echo esc_attr( $duration ); ?>" />
  </p>

<?php }

function kvkoolitus_prices_metabox_callback( $post ) { 

wp_nonce_field( 'kvkoolitus_prices_metabox_nonce', 'kvkoolitus_prices_nonce' ); ?>

  <?php         
    $price   = get_post_meta( $post->ID, 'kvkoolitus-price', true );
    $km      = get_post_meta( $post->ID, 'kvkoolitus-km', true );
  ?>

  <p>
  <label for="kvkoolitus_price"><?php _e('Price', 'kvkoolitus' ); ?></label><br/> 
  <input type="text" class="widefat" name="kvkoolitus_price" value="<?php echo esc_attr( $price ); ?>" />
  </p>   

  <p>
  <input type="checkbox" value="1" name="kvkoolitus_km" <?php checked( '1', $km ); ?> />
  <label for="kvkoolitus_km"><?php _e('Income Tax Included', 'kvkoolitus' ); ?></label><br/> 
  </p>  

<?php }

function kvkoolitus_dates_save_meta( $post_id ) {

  if( !isset( $_POST['kvkoolitus_dates_nonce'] ) || !wp_verify_nonce( $_POST['kvkoolitus_dates_nonce'],'kvkoolitus_dates_metabox_nonce') ) 
    return;

  if ( !current_user_can( 'edit_post', $post_id ))
    return;

  if ( isset($_POST['kvkoolitus_start_date']) ) {        
    update_post_meta($post_id, 'kvkoolitus-start', sanitize_text_field( $_POST['kvkoolitus_start_date']));      
  }  

  if ( isset($_POST['kvkoolitus_end_date']) ) {        
    update_post_meta($post_id, 'kvkoolitus-end', sanitize_text_field( $_POST['kvkoolitus_end_date'] ));      
  }

  if ( isset($_POST['kvkoolitus_duration']) ) {        
    update_post_meta($post_id, 'kvkoolitus-duration',  sanitize_text_field($_POST['kvkoolitus_duration']));      
  }

}
add_action('save_post', 'kvkoolitus_dates_save_meta');

function kvkoolitus_prices_save_meta( $post_id ) {

  if( !isset( $_POST['kvkoolitus_prices_nonce'] ) || !wp_verify_nonce( $_POST['kvkoolitus_prices_nonce'],'kvkoolitus_prices_metabox_nonce') ) 
    return;

  if ( !current_user_can( 'edit_post', $post_id ))
    return;

  if ( isset($_POST['kvkoolitus_price']) ) {        
    update_post_meta($post_id, 'kvkoolitus-price', sanitize_text_field($_POST['kvkoolitus_price']));      
  }

  if ( isset($_POST['kvkoolitus_km']) ) {        
    update_post_meta($post_id, 'kvkoolitus-km', sanitize_text_field($_POST['kvkoolitus_km']));      
  } else {
    delete_post_meta($post_id, 'kvkoolitus-km');
  }

}
add_action('save_post', 'kvkoolitus_prices_save_meta');