I had a similar issue with MRS broth before.
I later found out that MRS broth should not be autoclaved at 121 deg for this very reason.
Instead, modify the autoclave conditions to 110 or 115 degrees for 10 min.
The broth should be a little darker than golden brown. I believe I used to include the powdered glycine in the broth before autoclaving.
However, I never got Glycine to work well for my Lactobacillus species.
Instead I found that low concentrations of penicillin work far better as a cell wall weakening agent. However, it was much more toxic to the cells if left too long.
As I am sure you are aware, most strains require their own optimised conditions so you may have to tweak (increase/decrease) the concentrations if it does not work straight away.
A protocol for this is below, (from doi: 10.1111/2049-632X.12040.):
Electrocompetent L. salivarius cells were prepared using a modified version of the approach previously described by Sheehan et al. (2006); essentially, a stationary phase (16–18 h) culture was inoculated (1% v/v) into 50 mL of MRS.
Following 2 h incubation at 37 °C with shaking at 100rpm (or until OD600 0.25), penicillin was added to a final concentration of 8 microgram/mL , and the culture was incubated for a further 1.5 h (max time!) until reaching an OD600 of 0.4–0.6.
After holding on ice for 10 min, cells were harvested by centrifugation (4 °C at 1000 g), washed twice with 1-mL ice-cold 10 mM MgCl2 solution, once with ice-cold electroporation buffer (EB; 0.5 M Sucrose/10% Glycerol) and resuspended in 46 microL of the same EB buffer.
Electrocompetent cells were kept on ice and used within 30 min. Electroporation was carried out using a Gene Pulser X electroporator (Bio-Rad). Forty-six microlitre of competent cells were mixed with 4 microL of plasmid DNA (Total concentration of 1 microg plasmid DNA/ reaction) in a chilled 0.2-cm electrode gap electroporation cuvette (Bio-Rad) and incubated on ice for a minimum of 5 min. The cells within the cuvette were then subjected to the following electrical parameters: 1.75 kV, 600 Ω parallel resistance, and 25 lF capacitance. For phenotypic expression, the cells were immediately diluted with 0.95 mL of prewarmed MRS-SM buffer (MRS broth, 300 mM Sucrose, 80 mM MgCl2), transferred to a sterile PP tube (Sarstedt) and incubated at 37 °C without agitation for a minimum of 3 h. After incubation, dilutions were plated onto MRS agar containing selective antibiotics. Plates were examined after 48 h incubation at 37 °C for the presence of antibiotic resistant colonies.
Hope this helps